US20220009992A1 - T cell receptors specific for mesothelin and their use in immunotherapy - Google Patents

T cell receptors specific for mesothelin and their use in immunotherapy Download PDF

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US20220009992A1
US20220009992A1 US17/291,985 US201917291985A US2022009992A1 US 20220009992 A1 US20220009992 A1 US 20220009992A1 US 201917291985 A US201917291985 A US 201917291985A US 2022009992 A1 US2022009992 A1 US 2022009992A1
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cell
acid sequence
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Thomas M. Schmitt
Aude G. CHAPUIS
Philip D. Greenberg
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Juno Therapeutics Inc
Fred Hutchinson Cancer Center
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Fred Hutchinson Cancer Research Center
Juno Therapeutics Inc
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70503—Immunoglobulin superfamily
    • C07K14/7051—T-cell receptor (TcR)-CD3 complex
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K2239/00—Indexing codes associated with cellular immunotherapy of group A61K39/46
    • A61K2239/46—Indexing codes associated with cellular immunotherapy of group A61K39/46 characterised by the cancer treated
    • A61K2239/49—Breast
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/12—Materials from mammals; Compositions comprising non-specified tissues or cells; Compositions comprising non-embryonic stem cells; Genetically modified cells
    • A61K35/14—Blood; Artificial blood
    • A61K35/17—Lymphocytes; B-cells; T-cells; Natural killer cells; Interferon-activated or cytokine-activated lymphocytes
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/12—Materials from mammals; Compositions comprising non-specified tissues or cells; Compositions comprising non-embryonic stem cells; Genetically modified cells
    • A61K35/28—Bone marrow; Haematopoietic stem cells; Mesenchymal stem cells of any origin, e.g. adipose-derived stem cells
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/461—Cellular immunotherapy characterised by the cell type used
    • A61K39/4611—T-cells, e.g. tumor infiltrating lymphocytes [TIL], lymphokine-activated killer cells [LAK] or regulatory T cells [Treg]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/463—Cellular immunotherapy characterised by recombinant expression
    • A61K39/4632—T-cell receptors [TCR]; antibody T-cell receptor constructs
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/464—Cellular immunotherapy characterised by the antigen targeted or presented
    • A61K39/4643—Vertebrate antigens
    • A61K39/4644—Cancer antigens
    • A61K39/464466—Adhesion molecules, e.g. NRCAM, EpCAM or cadherins
    • A61K39/464468—Mesothelin [MSLN]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K45/00—Medicinal preparations containing active ingredients not provided for in groups A61K31/00 - A61K41/00
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
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    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70503—Immunoglobulin superfamily
    • C07K14/70539—MHC-molecules, e.g. HLA-molecules
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
    • C12N15/86—Viral vectors
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    • C12N5/00—Undifferentiated human, animal or plant cells, e.g. cell lines; Tissues; Cultivation or maintenance thereof; Culture media therefor
    • C12N5/06—Animal cells or tissues; Human cells or tissues
    • C12N5/0602—Vertebrate cells
    • C12N5/0634—Cells from the blood or the immune system
    • C12N5/0636—T lymphocytes
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N2510/00—Genetically modified cells

Definitions

  • the present disclosure relates to the field of biomedicine and, specifically, to methods and compositions useful for use in treating diseases or disorders in which cells express mesothelin, such as in cancer therapy.
  • embodiments of the present disclosure relate to methods and compositions of TCRs with high affinity against tumor-associated antigen mesothelin, T cells expressing such high affinity antigen specific TCRs, nucleic acids encoding the same, and methods of use for carrying out cellular immunotherapy including engineered T cells.
  • T cells that express self/tumor-reactive TCRs are subject to central and peripheral tolerance (see Stone and Kranz, Frontiers Immunol. 4:244, 2013), with relative TCR affinities varying widely between donors. Therefore, many matched donors must be screened to identify a sufficiently high-affinity tumor-specific T cell clone from which a TCR ⁇ / ⁇ gene therapy construct can be generated.
  • WT1 Wilms' Tumor antigen 1
  • FIG. 1A depicts identification and selection of TCRs specific for Msln 20 (SEQ ID NO:31) based on the fold-enrichment of TCRs to peptide:HLA tetramer binding. A TCR selected for further studies is circled.
  • FIG. 1B depicts identification and selection of TCRs specific for Msln 530 (SEQ ID NO:32) based on the fold-enrichment of tetramer from a pool of TCRs with binding to a Msln 530 :HLA tetramer. TCRs that were selected for further studies are circled.
  • FIG. 2 depicts tetramer binding by Msln 530 -specific TCRs (ranked by affinity, based on tetramer binding) in assays to determine whether or not cell-expressed TCR was able to detect the Msln 530 peptide:HLA complex in the presence or absence of the CD8 co-receptor.
  • CD8-independent binding correlates with high affinity of the respective T cell clone.
  • FIGS. 3A-3C show further functional testing of Msln-specific TCRs.
  • A Representative data of a T cell clone evaluated for antigen-driven activation based on a reporter cell line expressing the Nur77-tdTomato transgene, as measured by flow cytometry. Nur77 is an indicator of antigen receptor signaling in human T cells (see, e.g., Ashouri and Weiss, J. Immunol. 198(2):657-658 (2017)). In this assay, the T cell clone was incubated with T2 target cells that were pulsed with increasing concentrations of peptide, as indicated.
  • FIG. 4 shows functional evaluation of TCR clones in response to peptide, based on Nur77 tomato reporter activity.
  • TCRs including “B9” and “A11” (also referred to herein as “11A”), confer high antigen specificity despite exhibiting lower tetramer binding.
  • TCRs are ranked (left-to right and top-to-bottom) according to tetramer binding.
  • FIGS. 5A-5C show functional evaluation of TCRs heterologously expressed in primary CD8 + T cells.
  • CD8+ T cells were purified from donor PBMCs and lentivirally transduced with each TCR. After 8 days, cells that sorted high for tetramer-positive were further sorted and further expanded for 8-10 days.
  • FIGS. 6A-6C show characterization of primary CD8+ T cells that were transduced with the indicated Msln-specific TCR and assessed for functional activity upon incubation with peptide-pulsed T2 cells, as measured by interferon-gamma production (A, B). TCRs were ranked by the EC50, based on the amount of peptide pulsed into T2 cells (C).
  • FIGS. 7A-7D show specific lysis of two representative Msln-positive tumor cell lines ((A, B) MDA-MB-468 and (C, D) MDA-MB-231) by CD8+ T cells transduced with the indicated Msln 530 -specific TCR or with a Msln 20 -specific TCR and in the presence or absence of exogenous IFN- ⁇ .
  • FIG. 8 relates to an alanine mutagenesis scanning experiment to assess which amino acids of the target Msln 20 peptide (SEQ ID NO:31) are essential for effective binding and killing by exemplary Msln 20 -specific TCRs.
  • a series of variant peptides were generated in which an alanine was substituted for each successive position along the peptide of SEQ ID NO:31, and each variant peptide was assessed for IFN- ⁇ production by CD8+ T cells expressing the indicated Msln 20 -specific TCR.
  • positions 3-6 of SEQ ID NO:31 are essential for TCR binding.
  • an “X” indicates that a substitution mutation of the indicated residue in SEQ ID NO:31 to alanine does not impact or substantially impact functional binding of the TCR to its cognate peptide target.
  • FIGS. 9A-9D show results from alanine mutagenesis scanning experiments using TCRs specific for Msln 20 (SEQ ID NO:31) or Msln 530 (SEQ ID NO:32).
  • the x-axis shows the percent of IFN- ⁇ + T cells in response to each alanine-substituted peptide.
  • the y-axis shows the sequence of the tested peptide, wherein an X indicates that this residue is not required for TCR specificity, as indicated by near normal functional activity as compared to the wild-type peptide.
  • FIG. 10 shows human peptides (SEQ ID NOs: 63-77) that were investigated for potential cross-reactivity with the target Msln 530 peptide (SEQ ID NO:32), based on the specificity of the TCR as determined by alanine scanning experiments.
  • the genes encoding the indicated peptides are shown at the left of the table. Consensus sequences containing the essential residues identified by alanine scanning were input into prediction algorithms, as described in Example 8.
  • FIGS. 11A and 11B depict analysis of synthesized peptides with potential homology to Msln 530 in the human proteome.
  • the functional activity of two Msln 530 -specific TCRs ( FIG. 11A , FIG. 11B ) upon incubation with T2 cells pulsed with a high dose (10 ⁇ M) of peptide was measured by IFN- ⁇ .
  • a dose-dependent titration was performed to determine the EC50. TCRs were ranked by the EC50 based on the amount of peptide pulsed into T2 cells.
  • Peptide #10 is from a gene called EHF. This gene encodes a protein that belongs to an ETS transcription factor subfamily characterized by epithelial-specific expression. ETS acts as a transcriptional repressor, and may be involved in epithelial differentiation and carcinogenesis.
  • FIGS. 12A-12I depict experiments investigating the potential for alloreactivity of T cells expressing an exemplary Msln-specific TCR of the present disclosure (Meso20-3B, Meso530-11A, or Meso530-11B) by targeting diverse donor-derived lymphoblastoid cell lines (LCLs) in the presence of absence of wild-type peptide.
  • FIGS. 13A-13H depict additional analysis of alloreactivity by targeting diverse donor-derived LCLs to assess no cross-reactivity to other HLA subtypes, as described in Example 10.
  • Meso530-11B indicates potential reactivity in the presence of peptide (as highlighted in the table) for non HLA-A2 alleles.
  • the present disclosure provides binding proteins that comprise a TCR alpha chain variable domain (V ⁇ ) and a TCR beta chain variable domain (V ⁇ ) and are capable of specifically binding to a Msln 20-28 or Msln 530-538 epitope and/or peptide (Msln 20-28 (SLLFLLFSL; SEQ ID NO: 31)) and Msln 530-538 (SEQ ID NO:32 (VLPLTVAEV)) are also referred to herein as Msln 20 and M 530 , respectively); e.g., in a peptide:HLA complex.
  • V ⁇ TCR alpha chain variable domain
  • V ⁇ TCR beta chain variable domain
  • a Msln-specific binding protein is capable of binding to a Msln peptide:HLA complex, wherein the Msln peptide comprises the amino acid sequence set forth in SEQ ID NO:31 or 32 and wherein the HLA is or comprises HLA-A2, such as HLA-A*02:01.
  • a Msln-specific 20-28 -specific binding protein comprises: (a) a TCR V ⁇ comprising a CDR3 amino acid sequence as set forth in SEQ ID NO:33 or 35, and a TCR V ⁇ , wherein optionally the TCR V ⁇ has at least about 85% (i.e., at least about 85%, 86%, 87%, 89% 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more) identity to the amino acid sequence set forth in SEQ ID NO:95 or 97; (b) a TCR V ⁇ comprising a CDR3 amino acid sequence as set forth in SEQ ID NO:34 or 36, and (b) a TCR V ⁇ , wherein optionally the TCR V ⁇ has at least about 85% (i.e., at least about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 9
  • a sequence identity of “at least about” an indicated percentage includes the indicated percentage ⁇ 20% thereof, and every integer and non-integer percentage above the specific percentage. Accordingly, “at least about 85%” identity to the referenced sequence (e.g., any one of SEQ ID NOs:1-123) includes about 85%, 86%, 87%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identity to the referenced sequence, and also includes all non-integer percentages in between two integer percentages (e.g., 92.5%, 99.1%, etc.).
  • a Msln 20-28 -specific binding protein comprises a CDR3 ⁇ amino acid sequence as set forth in SEQ ID NO:33 and a CDR3 ⁇ amino acid sequence as set forth in SEQ ID NO:34.
  • the binding protein comprises a CDR1 ⁇ amino acid sequence as set forth SEQ ID NO:80, a CDR2 ⁇ amino acid sequence as set forth in SEQ ID NO:81 or 118, a CDR1 ⁇ amino acid sequence as set forth in any one of SEQ ID NOs:78, 82, 83, or 84, and a CDR2 ⁇ amino acid sequence as set forth in SEQ ID NO:79.
  • the V ⁇ comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:96, and/or the V ⁇ comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:95, wherein optionally there are no changes in CDR1 ⁇ , CDR2 ⁇ , CDR1 ⁇ , and/or CDR2 ⁇ .
  • the Msln 20-28 -specific binding protein comprises (i) a TCR V ⁇ comprising (a) an amino acid sequence having at least about 85% identity to an amino acid sequence encoded by TRBV12-4*01 (e.g., to a TRBV12-4*01-encoded amino acid sequence that is at least about 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, or 108 contiguous amino acids in length); and/or (b) an amino acid sequence having at least about 85% identity an amino acid sequence encoded by TRBJ2-7*01 (e.g., to a TRBJ2-7*01-encoded amino acid sequence that is at least about 5, 6, 7, 8, 9, 10, 11, 12, 13, or 14 amino acids long); and/or (ii) TCR V ⁇ comprising (a) an amino acid sequence having at least about 85% identity to an amino acid sequence encoded by TRAV1-1*01 (e.g., to
  • a TCR V ⁇ may include an amino acid sequence that is at least about 85% identical to an amino acid sequence encoded by TRBD1*01 or TRBD2*02.
  • TCR genes are known and can be found at, for example, imgt.org, which provides gene tables and nucleotide and amino acid sequences for human TRAV, TRBV, TRAJ, TRBJ, TRBD, TRAC, and TRBD alleles.
  • a Msln 20-28 -specific binding protein comprises a CDR3 ⁇ amino acid sequence as set forth in SEQ ID NO:36 and a CDR3 ⁇ amino acid sequence as set forth in SEQ ID NO:35.
  • the binding protein further comprises a CDR1 ⁇ amino acid sequence as set forth SEQ ID NO:85, a CDR2 ⁇ amino acid sequence as set forth in SEQ ID NO:86 or 119, a CDR1 ⁇ amino acid sequence as set forth in any one of SEQ ID NOs: 82, 83, or 84, and a CDR2 ⁇ amino acid sequence as set forth in SEQ ID NO:79.
  • the V ⁇ comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:98, and/or the V ⁇ comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:97, wherein there are optionally no changes in CDR1 ⁇ , CDR2 ⁇ , CDR1 ⁇ , and/or CDR2 ⁇ .
  • the Msln 20-28 -specific binding protein comprises a TCR V ⁇ comprising (a) an amino acid sequence having at least about 85% identity to an amino acid sequence encoded by TRAV12-3*01 (e.g., to a TRAV12-3*01-encoded amino acid sequence that is at least about 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, or 108 contiguous amino acids in length) and/or (b) an amino acid sequence having at least about 85% identity to an amino acid sequence encoded by TRA29*01 (e.g., to a TRAJ29*01-encoded amino acid sequence that is at least about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 amino acids long).
  • TRAV12-3*01 e.g., to a TRAV12-3*01-encoded amino acid sequence that is at least about 10, 15, 20, 25, 30, 35, 40, 45, 50, 55
  • alanine mutagenesis of any one or more of residues 1, 2, 7, 8, or 9 of SEQ ID NO:31 does not abrogate or does not substantially impair binding by a Msln 20-28 -specific binding protein.
  • a Msln 20-28 -specific binding protein is capable of binding to a peptide comprising or consisting of the consensus amino acid sequence set forth in SEQ ID NO:60; e.g., in a peptide:HLA complex as disclosed herein.
  • a Msln 530-538 -specific binding protein comprises: (a) a TCR V ⁇ comprising a CDR3 amino acid sequence as set forth in SEQ ID NO:37 or 39, and a TCR V ⁇ , wherein the TCR V ⁇ optionally has at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:99 or 101; (b) a TCR V ⁇ comprising a CDR3 amino acid sequence as set forth in SEQ ID NO:34 or 36, and (b) a TCR V ⁇ , wherein the TCR V ⁇ optionally has at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:100 or 102; or (c) a TCR V ⁇ comprising a CDR3 amino acid sequence as set forth in SEQ ID NO:37 or 39 and a TCR V ⁇ comprising a CDR3 amino acid sequence as set forth in SEQ ID NO:38 or 40.
  • a Msln 530-538 -specific binding protein comprises a CDR3 ⁇ amino acid sequence as set forth in SEQ ID NO:37 and a CDR3 ⁇ amino acid sequence as set forth in SEQ ID NO:38.
  • the binding protein further comprises a CDR1 ⁇ amino acid sequence as set forth SEQ ID NO:89, a CDR2 ⁇ amino acid sequence as set forth in SEQ ID NO:90, a CDR1 ⁇ amino acid sequence as set forth in any one of SEQ ID NOs: 83 or 87, and a CDR2 ⁇ amino acid sequence as set forth in SEQ ID NO:88.
  • the V ⁇ comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:100, and/or the V ⁇ comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:99, wherein optionally there are no changes in CDR1 ⁇ , CDR2 ⁇ , CDR1 ⁇ , and/or CDR2 ⁇ .
  • a Msln 530-538 -specific binding protein comprises a CDR3 ⁇ amino acid sequence as set forth in SEQ ID NO:39 and a CDR3 ⁇ amino acid sequence as set forth in SEQ ID NO:40.
  • the binding protein further comprises a CDR1 ⁇ amino acid sequence as set forth SEQ ID NO:93, a CDR2 ⁇ amino acid sequence as set forth in SEQ ID NO:94, a CDR1 ⁇ amino acid sequence as set forth in any one of SEQ ID NOs: 83, 84, or 91, and a CDR2 ⁇ amino acid sequence as set forth in SEQ ID NO:92.
  • the V ⁇ comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:102, and/or the V ⁇ comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:101, wherein there are optionally no changes in CDR1 ⁇ , CDR2 ⁇ , CDR1 ⁇ , and/or CDR2 ⁇ .
  • the Msln 530-538 -specific binding protein comprises a TCR V ⁇ comprising an amino acid sequence having at least about 85% identity to an amino acid sequence encoded by TRBJ2-3*01 (e.g., to a TRBJ2-3*01-encoded amino acid sequence that is at least about 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 15 contiguous amino acids in length).
  • alanine mutagenesis of any one or more of residues 3, 5, 6, or 9 of SEQ ID NO:32 does not abrogate or does not substantially impair binding by a Msln 530-538 -specific binding protein.
  • a Msln 530-538 -specific binding protein is capable of binding to a peptide comprising or consisting of the consensus amino acid sequence set forth in SEQ ID NO:61; e.g., in a peptide:HLA complex as disclosed herein.
  • alanine mutagenesis of any one or more of residues 1, 5, or 9 of SEQ ID NO:32 does not abrogate or does not substantially impair binding by a Msln 530-538 -specific binding protein.
  • a Msln 530-538 -specific binding protein is capable of binding to a peptide comprising or consisting of the consensus amino acid sequence set forth in SEQ ID NO:62; e.g., in a peptide:HLA complex as disclosed herein.
  • a Msln 530-538 -specific binding protein of the present disclosure does not bind, or does not specifically bind relative to Msln 530-538 , to a peptide:HLA complex wherein the peptide comprises or consists of the amino acid sequence set forth in any one or more of SEQ ID NOs:63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, and 77, and wherein the HLA optionally comprises an HLA-A2, such as HLA-A:02*01.
  • a Msln-specific binding protein i.e., Msln 20-28 -specific binding protein, Msln 530-538 -specific binding protein
  • Msln 20-28 -specific binding protein Msln 530-538 -specific binding protein
  • Msln peptide:HLA complex as disclosed herein in the absence of, or independent of, CD8.
  • a binding protein (e.g., when expressed on the cell surface of a human T cell) has a Msln peptide EC50 of about 9 ⁇ M, about 8 ⁇ M, about 7 ⁇ M, about 6 ⁇ M, about 5 ⁇ M, about 4 ⁇ M, about 3 ⁇ M, about 2 ⁇ M, about 1 ⁇ M, about 0.9 ⁇ M, about 0.8 ⁇ M, about 0.7 ⁇ M, about 0.6 ⁇ M, about 0.5 ⁇ M, about 0.4 ⁇ M, about 0.3 ⁇ M, about 0.2 ⁇ M, or less.
  • Msln-specific binding proteins are non-alloreactive against various human HLA types in the absence of a Msln peptide antigen.
  • an immune cell e.g., a T cell
  • a Msln-specific binding protein of this disclosure does not produce IFN- ⁇ and/or does not exhibit activation (e.g., CD8 expression, CD3 expression, Nur77 expression) and/or cytotoxic activity (e.g., specific killing, production and release of a perforin and/or a granzyme) when contacted with a cell expressing: (i) HLA-C6:02:01; (ii) HLA-B13:01:01 without HLA-B13:02:01; (iii) HLA-A3; (iv) HLA-A29; (v) HLA-B40; (vi) HLA-B44; (vii) HLA-C3; (viii) HLA-C16; (ix) HLA-A1; (x) HLA
  • compositions and recombinant host cells including, encoding, and/or expressing the binding proteins are also provided.
  • a binding protein is capable of expression on a cell surface by a host T cell.
  • binding by a Msln-specific binding protein that is expressed on the surface of an immune cell (e.g., a T cell) to a Msln peptide:HLA complex activates the immune cell, wherein activation is optionally determined by Nur77 expression and/or activity.
  • the presently disclosed binding proteins are highly sensitive for a cognate Mlsn peptide antigen.
  • Nur77 expression is increased when the immune cell is in the presence of about 10 ⁇ 2 ⁇ M peptide, about 10 ⁇ 1 ⁇ M peptide, about 1 ⁇ M peptide, or about 10 1 ⁇ M peptide, wherein the peptide is optionally presented by an antigen presenting cell; i.e., in a peptide:HLA complex.
  • a binding protein-encoding polynucleotide comprises a polynucleotide having at least about 50% sequence identity (i.e., at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 86%, 87%, 89% 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more) to the polynucleotide sequence set forth in any one of SEQ ID NOS: 1-5, 9-13, 17-21, 25-27, and 120.
  • Vectors that contain a polynucleotide are also provided.
  • binding proteins, and recombinant host cells, and related compositions may be used to treat a subject having a disease or disorder associated with mesothelin expression and/or activity, such as for example, a cancer.
  • a cancer is a solid cancer.
  • the solid cancer is or comprises biliary cancer, bladder cancer, bone and soft tissue carcinoma, brain tumor, breast cancer, cervical cancer, colon cancer, colorectal adenocarcinoma, colorectal cancer, desmoid tumor, embryonal cancer, endometrial cancer, esophageal cancer, gastric cancer, gastric adenocarcinoma, glioblastoma multiforme, gynecological tumor, head and neck squamous cell carcinoma, hepatic cancer, lung cancer, mesothelioma, malignant melanoma, osteosarcoma, ovarian cancer, pancreatic cancer, pancreatic ductal adenocarcinoma, primary astrocytic tumor, primary thyroid cancer, prostate cancer, renal cancer, renal cell carcinoma, rhabdomyosarcoma, skin cancer, soft tissue sarcoma, testicular germ-cell tumor, urothelial cancer, uterine sarcoma, or uter
  • compositions and recombinant host cells may be used to treat a cancer wherein an Msln 20-28 peptide is expressed on a tumor cell of the cancer, or a cancer wherein an Msln 530-538 peptide is expressed on a tumor cell of the cancer, such as, for example, mesothelioma, pancreatic cancer, ovarian cancer, or lung cancer.
  • polynucleotides that encode a binding protein as provided herein are also provided herein, and polynucleotides that encode a binding protein as provided herein, vectors that comprise a binding-protein-encoding polynucleotide, and host cells that comprise a vector.
  • any concentration range, percentage range, ratio range, or integer range is to be understood to include the value of any integer within the recited range and, when appropriate, fractions thereof (such as one tenth and one hundredth of an integer), unless otherwise indicated.
  • any number range recited herein relating to any physical feature, such as polymer subunits, size or thickness is to be understood to include any integer within the recited range, unless otherwise indicated.
  • “About,” as used herein, when referring to a measurable value, range, or structure, is meant to encompass variations of ⁇ 20%, ⁇ 10%, ⁇ 5%, ⁇ 1%, or ⁇ 0.1% from the specified value, unless otherwise indicated.
  • a protein domain, region, or module e.g., a binding domain, hinge region, or linker
  • a protein which may have one or more domains, regions, or modules
  • amino acid refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids.
  • Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, ⁇ -carboxyglutamate, and O-phosphoserine.
  • Amino acid analogs refer to compounds that have the same basic chemical structure as a naturally occurring amino acid, i.e., an ⁇ -carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs have modified R groups (e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid.
  • Amino acid mimetics refer to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that function in a manner similar to a naturally occurring amino acid.
  • mutation refers to a change in the sequence of a nucleic acid molecule or polypeptide molecule as compared to a reference or wild-type nucleic acid molecule or polypeptide molecule, respectively.
  • a mutation can result in several different types of change in sequence, including substitution, insertion or deletion of nucleotide(s) or amino acid(s).
  • a mutation is a substitution of one or three codons or amino acids, a deletion of one to about 5 codons or amino acids, or a combination thereof.
  • a “conservative substitution” refers to amino acid substitutions that do not significantly affect or alter binding characteristics of a particular protein. Generally, conservative substitutions are ones in which a substituted amino acid residue is replaced with an amino acid residue having a similar side chain. Conservative substitutions include a substitution found in one of the following groups: Group 1: Alanine (Ala or A), Glycine (Gly or G), Serine (Ser or S), Threonine (Thr or T); Group 2: Aspartic acid (Asp or D), Glutamic acid (Glu or Z); Group 3: Asparagine (Asn or N), Glutamine (Gln or Q); Group 4: Arginine (Arg or R), Lysine (Lys or K), Histidine (His or H); Group 5: Isoleucine (Ile or I), Leucine (Leu or L), Methionine (Met or M), Valine (Val or V); and Group 6: Phenylalanine (Phe or F), Tyrosine (Tyr or
  • amino acids can be grouped into conservative substitution groups by similar function, chemical structure, or composition (e.g., acidic, basic, aliphatic, aromatic, or sulfur-containing).
  • an aliphatic grouping may include, for purposes of substitution, Gly, Ala, Val, Leu, and Ile.
  • conservative substitutions groups include: sulfur-containing: Met and Cysteine (Cys or C); acidic: Asp, Glu, Asn, and Gln; small aliphatic, nonpolar or slightly polar residues: Ala, Ser, Thr, Pro, and Gly; polar, negatively charged residues and their amides: Asp, Asn, Glu, and Gln; polar, positively charged residues: His, Arg, and Lys; large aliphatic, nonpolar residues: Met, Leu, Ile, Val, and Cys; and large aromatic residues: Phe, Tyr, and Trp. Additional information can be found in Creighton (1984) Proteins, W.H. Freeman and Company. Variant proteins, peptides, polypeptides, and amino acid sequences of the present disclosure can, in certain embodiments, comprise one or more conservative substitutions relative to a reference amino acid sequence.
  • protein or “polypeptide” refers to a polymer of amino acid residues. Proteins apply to naturally occurring amino acid polymers, as well as to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid and non-naturally occurring amino acid polymers.
  • fusion protein refers to a protein that, in a single chain, has at least two distinct domains or motifs, wherein the domains or motifs are not naturally found together (e.g., in the specified arrangement, order, or number, or at all) in a protein.
  • a fusion protein comprises at least two distinct domains or motifs that are not naturally found together in a single peptide or polypeptide.
  • a polynucleotide encoding a fusion protein may be constructed using PCR, recombinantly engineered, or the like, or such fusion proteins can be synthesized.
  • a fusion protein may further contain other components, such as a tag, a linker, or a transduction marker.
  • a fusion protein expressed or produced by a host cell locates to the cell surface, where the fusion protein is anchored to the cell membrane (e.g., via a transmembrane domain) and comprises an extracellular portion or component (e.g., containing a binding domain and, in certain embodiments, a linker, a spacer, or both) and an intracellular portion or component.
  • “Junction amino acids” or “junction amino acid residues” refer to one or more (e.g., about 2-10) amino acid residues between two adjacent motifs, regions, or domains of a polypeptide, such as between a binding domain and an adjacent constant domain or between a TCR chain and an adjacent self-cleaving peptide. Junction amino acids may result from the construct design of a fusion protein (e.g., amino acid residues resulting from the use of a restriction enzyme site during the construction of a nucleic acid molecule encoding a fusion protein).
  • Nucleic acid molecule refers to a polymeric compound including covalently linked nucleotides, which can be made up of natural subunits (e.g., purine or pyrimidine bases) or non-natural subunits (e.g., morpholine ring).
  • Purine bases include adenine, guanine, hypoxanthine, and xanthine
  • pyrimidine bases include uracil, thymine, and cytosine.
  • Nucleic acid molecules include polyribonucleic acid (RNA), polydeoxyribonucleic acid (DNA), which includes cDNA, genomic DNA, and synthetic DNA, either of which may be single or double-stranded.
  • the nucleic acid molecule may be the coding strand or non-coding (anti-sense strand).
  • a nucleic acid molecule encoding an amino acid sequence includes all nucleotide sequences that encode the same amino acid sequence. Some versions of the nucleotide sequences may also include intron(s) to the extent that the intron(s) would be removed through co- or post-transcriptional mechanisms. In other words, different nucleotide sequences may encode the same amino acid sequence as the result of the redundancy or degeneracy of the genetic code, or by splicing.
  • Variants of nucleic acid molecules of this disclosure are also contemplated. Variant nucleic acid molecules are at least 70%, 75%, 80%, 85%, 90%, and are preferably 95%, 96%, 97%, 98%, 99%, or 99.9% identical a nucleic acid molecule of a defined or reference polynucleotide as described herein, or that hybridize to a polynucleotide under stringent hybridization conditions of 0.015 M sodium chloride, 0.0015 M sodium citrate at about 65-68° C. or 0.015 M sodium chloride, 0.0015 M sodium citrate, and 50% formamide at about 42° C. Nucleic acid molecule variants retain the capacity to encode a fusion protein or a binding domain thereof having a functionality described herein, such as specifically binding a target molecule.
  • Percent sequence identity refers to a relationship between two or more sequences, as determined by comparing the sequences. Preferred methods to determine sequence identity are designed to give the best match between the sequences being compared. For example, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment). Further, non-homologous sequences may be disregarded for comparison purposes. The percent sequence identity referenced herein is calculated over the length of the reference sequence, unless indicated otherwise. Methods to determine sequence identity and similarity can be found in publicly available computer programs.
  • Sequence alignments and percent identity calculations may be performed using a BLAST program (e.g., BLAST 2.0, BLASTP, BLASTN, or BLASTX).
  • BLAST program e.g., BLAST 2.0, BLASTP, BLASTN, or BLASTX.
  • the mathematical algorithm used in the BLAST programs can be found in Altschul et al., Nucleic Acids Res. 25:3389-3402, 1997.
  • sequence analysis software is used for analysis, the results of the analysis are based on the “default values” of the program referenced. “Default values” mean any set of values or parameters which originally load with the software when first initialized.
  • similarity between two polypeptides is determined by comparing the amino acid sequence and conserved amino acid substitutes thereto of the polypeptide to the sequence of a second polypeptide (e.g., using GENEWORKSTM, Align, ClustalTM, the BLAST algorithm, or the like). In certain embodiments, the BLAST algorithm is preferred.
  • isolated means that the material is removed from its original environment (e.g., the natural environment if it is naturally occurring).
  • a naturally occurring nucleic acid or polypeptide present in a living animal is not isolated, but the same nucleic acid or polypeptide, separated from some or all of the co-existing materials in the natural system, is isolated.
  • Such nucleic acid could be part of a vector and/or such nucleic acid or polypeptide could be part of a composition (e.g., a cell lysate), and still be isolated in that such vector or composition is not part of the natural environment for the nucleic acid or polypeptide.
  • gene means the segment of DNA involved in producing a polypeptide chain; it includes regions preceding and following the coding region (“leader and trailer”) as well as intervening sequences (introns) between individual coding segments (exons).
  • the term “variant” as used herein refers to at least one fragment of the full length sequence referred to, more specifically one or more amino acid or nucleic acid sequence which is, relative to the full-length sequence, truncated at one or both termini by one or more amino acids.
  • a fragment includes or encodes for a peptide having at least 6, 7, 8, 10, 12, 15, 20, 25, 50, 75, 100, 150, or 200 successive amino acids of the original sequence or a variant thereof.
  • the total length of the variant may be at least 6, 7, 8, 9, 10, 11, 12, 20, 25, 30, 40, 50, 60, 70, 80, 90, 100, or more amino acids.
  • the term “variant” relates not only to at least one fragment, but also to a polypeptide or a fragment thereof including amino acid sequences that are at least 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to the reference amino acid sequence referred to or the fragment thereof, wherein amino acids other than those essential for the biological activity or the fold or structure of the polypeptide are deleted or substituted, one or more such essential amino acids are replaced in a conservative manner, and/or amino acids are added such that the biological activity of the polypeptide is preserved.
  • the state of the art includes various methods that may be used to align two given nucleic acid or amino acid sequences and to calculate the degree of identity (see, e.g., Arthur Lesk (2008), Introduction to bioinformatics, Oxford University Press, 2008, 3rd edition).
  • the Clustal W software can be used using default settings (Larkin, M. A., et al. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948).
  • variants may, in addition, include chemical modifications, for example, isotopic labels or covalent modifications such as glycosylation, phosphorylation, acetylation, decarboxylation, citrullination, hydroxylation and the like.
  • chemical modifications for example, isotopic labels or covalent modifications such as glycosylation, phosphorylation, acetylation, decarboxylation, citrullination, hydroxylation and the like.
  • the term “variant” of a nucleic acid molecule includes nucleic acids the complementary strand of which hybridizes, for example, under stringent conditions, to the reference or wild type nucleic acid.
  • Stringency of hybridization reactions is readily determinable by one of ordinary skill in the art, and in general is an empirical calculation dependent on probe length, washing temperature, and salt concentration. In general, longer probes require higher temperatures for proper annealing, while shorter probes less so.
  • Hybridization generally depends on the ability of denatured DNA to reanneal to complementary strands present in an environment below their melting temperature: the higher the degree of desired homology between the probe and hybridizable sequence, the higher the relative temperature which may be used.
  • stringent conditions are applied for any hybridization, i.e., hybridization occurs only if the probe is 70% or more identical to the target sequence.
  • Probes having a lower degree of identity with respect to the target sequence may hybridize, but such hybrids are unstable and will be removed in a washing step under stringent conditions, for example, lowering the concentration of salt to 2 ⁇ SSC or, optionally and subsequently, to 0.5 ⁇ SSC, while the temperature is, for example, about 50° C.-68° C., about 52° C.-68° C., about 54° C.-68° C., about 56° C.-68° C., about 58° C.-68° C., about 60° C.-68° C., about 62° C.-68° C., about 64° C.-68° C., or about 66° C.-68° C.
  • the temperature is about 64° C.-68° C. or about 66° C.-68° C. It is possible to adjust the concentration of salt to 0.2 ⁇ SSC or even 0.1 ⁇ SSC. Nucleic acid sequences having a degree of identity with respect to the reference or wild type sequence of at least 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5% may be isolated.
  • the term variant of a nucleic acid sequence refers to any nucleic acid sequence that encodes the same amino acid sequence and variants thereof as the reference nucleic acid sequence, in line with the degeneracy of the genetic code.
  • a “functional variant” refers to a polypeptide or polynucleotide that is structurally similar or substantially structurally similar to a parent or reference compound of this disclosure, but differs, in some contexts slightly, in composition (e.g., one base, atom or functional group is different, added, or removed; or one or more amino acids are mutated, inserted, or deleted), such that the polypeptide or encoded polypeptide is capable of performing at least one function of the encoded parent polypeptide with at least 50% efficiency, preferably at least 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9%, or 100% level of activity of the parent polypeptide.
  • a functional variant of a polypeptide or encoded polypeptide of this disclosure has “similar binding,” “similar affinity” or “similar activity” when the functional variant displays no more than a 50% reduction in performance in a selected assay as compared to the parent or reference polypeptide, such as an assay for measuring binding affinity (e.g., Biacore® or tetramer staining measuring an association (Ka) or a dissociation (KD) constant), avidity, or activation of a host cell.
  • binding affinity e.g., Biacore® or tetramer staining measuring an association (Ka) or a dissociation (KD) constant
  • a “functional portion” or “functional fragment” refers to a polypeptide or polynucleotide that comprises only a domain, motif, portion or fragment of a parent or reference compound, and the polypeptide or encoded polypeptide retains at least 50% activity associated with the domain, portion or fragment of the parent or reference compound, preferably at least 55%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9%, or 100% level of activity of the parent polypeptide, or provides a biological benefit (e.g., effector function).
  • a biological benefit e.g., effector function
  • a “functional portion” or “functional fragment” of a polypeptide or encoded polypeptide of this disclosure has “similar binding” or “similar activity” when the functional portion or fragment displays no more than a 50% reduction in performance in a selected assay as compared to the parent or reference polypeptide (preferably no more than 20% or 10%, or no more than a log difference as compared to the parent or reference with regard to affinity), such as an assay for measuring binding affinity or measuring effector function (e.g., cytokine release).
  • a functional portion refers to a “signaling portion” of an effector molecule, effector domain, costimulatory molecule, or costimulatory domain.
  • altered domain refers to a motif, region, domain, peptide, polypeptide, or protein with a non-identical sequence identity to a wild type motif, region, domain, peptide, polypeptide, or protein (e.g., a wild type TCR ⁇ chain, TCR ⁇ chain, TCR ⁇ constant domain, or TCR ⁇ constant domain) of at least 85% (e.g., 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9%).
  • a wild type motif, region, domain, peptide, polypeptide, or protein e.g., a wild type TCR ⁇ chain, TCR ⁇ chain, TCR ⁇ constant domain, or TCR ⁇ constant domain
  • heterologous or “non-endogenous” or “exogenous” refers to any gene, protein, compound, nucleic acid molecule, or activity that is not native to a host cell or a subject, or any gene, protein, compound, nucleic acid molecule, or activity native to a host cell or a subject that has been altered.
  • Heterologous, non-endogenous, or exogenous includes genes, proteins, compounds, or nucleic acid molecules that have been mutated or otherwise altered such that the structure, activity, or both is different as between the native and altered genes, proteins, compounds, or nucleic acid molecules.
  • heterologous, non-endogenous, or exogenous genes, proteins, or nucleic acid molecules may not be endogenous to a host cell or a subject, but instead nucleic acids encoding such genes, proteins, or nucleic acid molecules may have been added to a host cell by conjugation, transformation, transfection, electroporation, or the like, wherein the added nucleic acid molecule may integrate into a host cell genome or can exist as extra-chromosomal genetic material (e.g., as a plasmid or other self-replicating vector).
  • the polynucleotide is “heterologous” to progeny of the host cell, whether or not the progeny were themselves manipulated (e.g., transduced) to contain the polynucleotide.
  • homologous refers to a gene, protein, compound, nucleic acid molecule, or activity found in or derived from a host cell, species, or strain.
  • a heterologous or exogenous polynucleotide or gene encoding a polypeptide may be homologous to a native polynucleotide or gene and encode a homologous polypeptide or activity, but the polynucleotide or polypeptide may have an altered structure, sequence, expression level, or any combination thereof.
  • a non-endogenous polynucleotide or gene, as well as the encoded polypeptide or activity may be from the same species, a different species, or a combination thereof.
  • endogenous or “native” refers to a polynucleotide, gene, protein, compound, molecule, or activity that is normally present in a host cell or a subject.
  • expression refers to the process by which a polypeptide is produced based on the encoding sequence of a nucleic acid molecule, such as a gene.
  • the process may include transcription, post-transcriptional control, post-transcriptional modification, translation, post-translational control, post-translational modification, or any combination thereof.
  • An expressed nucleic acid molecule is typically operably linked to an expression control sequence (e.g., a promoter).
  • operably linked refers to the association of two or more nucleic acid molecules on a single nucleic acid fragment so that the function of one is affected by the other.
  • a promoter is operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence (i.e., the coding sequence is under the transcriptional control of the promoter).
  • Unlinked means that the associated genetic elements are not closely associated with one another and the function of one does not affect the other.
  • the term “introduced” in the context of inserting a nucleic acid molecule into a cell means “transfection”, or “transformation” or “transduction” and includes reference to the incorporation of a nucleic acid molecule into a eukaryotic or prokaryotic cell wherein the nucleic acid molecule may be incorporated into the genome of a cell (e.g., chromosome, plasmid, plastid, or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (e.g., transfected mRNA).
  • a cell e.g., chromosome, plasmid, plastid, or mitochondrial DNA
  • transiently expressed e.g., transfected mRNA
  • the term “engineered,” “recombinant” or “non-natural” or “modified” refers to an organism, microorganism, cell, nucleic acid molecule, or vector that includes at least one genetic alteration or has been modified by introduction of an exogenous nucleic acid molecule, wherein such alterations or modifications are introduced by genetic engineering (i.e., human intervention). Genetic alterations include, for example, modifications introducing expressible nucleic acid molecules encoding proteins, fusion proteins or enzymes, or other nucleic acid molecule additions, deletions, substitutions or other functional disruption of a cell's genetic material.
  • Additional modifications include, for example, non-coding regulatory regions in which the modifications alter expression of a polynucleotide, gene or operon; e.g., such that expression of an endogenous nucleic acid molecule or gene is controlled, deregulated, or constitutive, where such alterations or modifications may be introduced by genetic engineering.
  • Genetic alterations may include, for example, modifications introducing nucleic acid molecules (which may include an expression control element, such as a promoter) encoding one or more proteins or enzymes, or other nucleic acid molecule additions, deletions, substitutions, or other functional disruption of or addition to a cell's genetic material.
  • Exemplary modifications include those in coding regions or functional fragments thereof of heterologous or homologous polypeptides from a reference or parent molecule.
  • more than one heterologous nucleic acid molecule can be introduced into a host cell as separate nucleic acid molecules, as a plurality of individually controlled genes, as a polycistronic nucleic acid molecule, as a single nucleic acid molecule encoding a fusion protein, or any combination thereof.
  • the two or more heterologous nucleic acid molecules can be introduced as a single nucleic acid molecule (e.g., on a single vector), on separate vectors, integrated into the host chromosome at a single site or multiple sites, or any combination thereof.
  • the number of referenced heterologous nucleic acid molecules or protein activities refers to the number of encoding nucleic acid molecules or the number of protein activities, not the number of separate nucleic acid molecules introduced into a host cell.
  • construct refers to any polynucleotide that contains a recombinant nucleic acid molecule.
  • a construct may be present in a vector (e.g., a bacterial vector, a viral vector) or may be integrated into a genome.
  • a “vector” is a nucleic acid molecule that is capable of transporting another nucleic acid molecule.
  • Vectors may be, for example, plasmids, cosmids, viruses, a RNA vector or a linear or circular DNA or RNA molecule that may include chromosomal, non-chromosomal, semi-synthetic or synthetic nucleic acid molecules.
  • Vectors of the present disclosure also include transposon systems (e.g., Sleeping Beauty, see, e.g., Geurts et al., Mol. Ther. 8:108, 2003: Mates et al., Nat. Genet. 41:753, 2009).
  • Exemplary vectors are those capable of autonomous replication (episomal vector), capable of delivering a polynucleotide to a cell genome (e.g., viral vector), or capable of expressing nucleic acid molecules to which they are linked (expression vectors).
  • a host refers to a cell (e.g., an immune system cell as described herein) or microorganism targeted for genetic modification with a heterologous nucleic acid molecule to produce a polypeptide of interest.
  • a host cell may optionally already possess or be modified to include other genetic modifications that confer desired properties related or unrelated to, e.g., biosynthesis of the heterologous protein (e.g., inclusion of a detectable marker; deleted, altered or truncated endogenous TCR; or increased co-stimulatory factor expression).
  • binding domain refers to a molecule, such as a peptide, oligopeptide, polypeptide, or protein that possesses the ability to specifically and non-covalently associate, unite, or combine with a target molecule (e.g., Msln 20-28 peptide (SEQ ID NO:31) or Msln 530-538 peptide (SEQ ID NO:32), in certain embodiments, in a complex with an HLA molecule).
  • a binding domain includes any naturally occurring, synthetic, semisynthetic, or recombinantly produced binding partner for a biological molecule or other target of interest.
  • the binding domain is an antigen-binding domain, such as an antibody or TCR or functional binding domain or antigen-binding fragment thereof.
  • binding domains include single chain antibody variable regions (e.g., single domain antibodies, sFv, scFv, and Fab), receptor ectodomains (e.g., TNF- ⁇ ), ligands (e.g., cytokines and chemokines), antigen-binding regions of TCRs, such as single chain TCRs (scTCRs), synthetic polypeptides selected for the specific ability to bind to a biological molecule, aptamers, or single domain antibodies (e.g., camelid or fish derived single domain antibodies; see, e.g., Arbabi-Ghahroudi M (2017) Front. Immunol. 8:1589).
  • single chain antibody variable regions e.g., single domain antibodies, sFv, scFv, and Fab
  • receptor ectodomains e.g.,
  • variable region refers to the domain of a TCR ⁇ -chain or ⁇ -chain (or ⁇ -chain and ⁇ -chain for ⁇ TCRs), or of an antibody heavy or light chain, that is involved in binding to antigen (i.e., contains amino acids and/or other structures that contact antigen and result in binding).
  • the variable domains of the ⁇ -chain and ⁇ -chain (V ⁇ and V ⁇ , respectively) of a native TCR generally have similar structures, with each domain comprising four generally conserved framework regions (FRs) and three CDRs.
  • Variable domains of antibody heavy (V H ) and light (V L ) chains each also generally comprise four generally conserved framework regions (FRs) and three CDRs. In both TCRs and antibodies, framework regions separate CDRs and CDRs are situated between framework regions (i.e., in primary structure).
  • variable domains of the ⁇ -chain and ⁇ -chain (V ⁇ and V ⁇ , respectively) of a native TCR generally have similar structures, with each domain comprising four conserved framework regions (FRs) and three CDRs.
  • the V ⁇ domain is encoded by two separate DNA segments, the variable gene segment and the joining gene segment (V-J); the V ⁇ domain is encoded by three 5 separate DNA segments, the variable gene segment, the diversity gene segment, and the joining gene segment (V-D-J).
  • Human TCR V, D, and J alleles, including the nucleotide and encoded amino acid sequences thereof, are known in the art.
  • a single V ⁇ or V ⁇ domain may be sufficient to confer antigen-binding specificity.
  • TCRs that bind a particular antigen may be isolated using a V ⁇ or V ⁇ domain from a TCR that binds the antigen to screen a library of complementary V ⁇ or V ⁇ domains, respectively.
  • CDR complementarity determining region
  • HVR hypervariable region
  • framework amino acids can also contribute to binding, e.g., may also contact the antigen or antigen-containing molecule.
  • there are three CDRs in each variable region i.e., three CDRs in each of the TCR ⁇ -chain and ⁇ -chain variable regions; 3 CDRs in each of the antibody heavy chain and light chain variable regions).
  • CDR3 is thought to be the main CDR responsible for recognizing processed antigen.
  • CDR1 and CDR2 mainly, or in some cases exclusively, interact with the MHC.
  • Variable domain sequences can be aligned to a numbering scheme (e.g., Kabat, EU, International Immunogenetics Information System (IMGT) and Aho), which can allow equivalent residue positions to be annotated and for different molecules to be compared using Antigen receptor Numbering And Receptor Classification (ANARCI) software tool (2016, Bioinformatics 15:298-300).
  • IMGT International Immunogenetics Information System
  • Aho Antigen receptor Numbering And Receptor Classification
  • CDRs are numbered according to the IMGT numbering system.
  • binding domains refers to an association or union of a binding domain, or of a protein comprising the same, to a target molecule with an affinity or K a (i.e., an equilibrium association constant of a particular binding interaction with units of 1/M) equal to or greater than 10 5 M ⁇ 1 , while not significantly associating or uniting with any other molecules or components in a sample.
  • Binding domains (or fusion proteins thereof) may be classified as “high affinity” binding domains (or fusion proteins thereof) or “low affinity” binding domains (or fusion proteins thereof).
  • “High affinity” binding domains refer to those binding domains with a K a of at least 10 7 M ⁇ 1 , at least 10 8 M ⁇ 1 , at least 10 9 M ⁇ 1 , at least 10 10 M ⁇ 1 , at least 10 11 M ⁇ 1 , at least 10 12 M ⁇ 1 , or at least 10 13 M ⁇ 1 .
  • “Low affinity” binding domains refer to those binding domains with a K a of up to 10 7 M ⁇ 1 , up to 10 6 M ⁇ 1 , or up to 10 5 M ⁇ 1 .
  • affinity may be defined as an equilibrium dissociation constant (K d ) of a particular binding interaction with units of M (e.g., 10 ⁇ 5 M to 10 ⁇ 13 M).
  • a binding domain may have “enhanced affinity,” which refers to a selected or engineered binding domain with stronger binding to a target antigen than a wild type (or parent) binding domain.
  • enhanced affinity may be due to a K a (equilibrium association constant) for the target antigen that is higher than the wild type binding domain, or due to a K d for the target antigen that is less than that of the wild type binding domain, or due to an off-rate (K off ) for the target antigen that is less than that of the wild type binding domain.
  • binding domains of the present disclosure that specifically bind a particular target, as well as determining binding domain or fusion protein affinities, such as western blot, ELISA, and BIACORE® analysis (see also, e.g., Scatchard, et al., Ann. N. Y. Acad. Sci. 57:660, 1949; and U.S. Pat. Nos. 5,283,173, 5,468,614, or the equivalent).
  • apparent affinity for a TCR is measured by assessing binding to various concentrations of tetramers, for example, by flow cytometry using labeled tetramers.
  • apparent K d of a TCR is measured using 2-fold dilutions of labeled tetramers (i.e., peptide:MHC tetramers) at a range of concentrations, followed by determination of binding curves by non-linear regression, apparent K d being determined as the concentration of ligand that yielded half-maximal binding.
  • a Msln 20-28 - or Msln 530-538 -specific binding protein includes a Msln 20-28 - or Msln 530-538 -specific immunoglobulin superfamily binding protein or binding portion thereof, respectively.
  • MHC-peptide tetramer staining refers to an assay used to detect antigen-specific T cells, which features a tetramer of MHC molecules, each including an identical peptide having an amino acid sequence that is cognate (e.g., identical or related to) at least one epitope (e.g., Msln 20-28 or Msln 530-538 ), wherein the complex is capable of binding TCRs specific for the cognate epitope.
  • Each of the MHC molecules may be tagged with a biotin molecule. Biotinylated MHC/peptides are tetramer zed by the addition of streptavidin, which can be fluorescently labeled.
  • the tetramer may be detected by flow cytometry via the fluorescent label.
  • an MHC-peptide tetramer assay is used to detect or select enhanced affinity TCRs of the instant disclosure.
  • Levels of cytokines may be determined according to methods described herein and practiced in the art, including for example, ELISA, ELISpot, intracellular cytokine staining, and flow cytometry and combinations thereof (e.g., intracellular cytokine staining and flow cytometry).
  • Immune cell proliferation and clonal expansion resulting from an antigen-specific elicitation or stimulation of an immune response may be determined by isolating lymphocytes, such as circulating lymphocytes in samples of peripheral blood cells or cells from lymph nodes, stimulating the cells with antigen, and measuring cytokine production, cell proliferation, and/or cell viability, such as by incorporation of tritiated thymidine or non-radioactive assays, such as MTT assays and the like.
  • lymphocytes such as circulating lymphocytes in samples of peripheral blood cells or cells from lymph nodes
  • stimulating the cells with antigen and measuring cytokine production, cell proliferation, and/or cell viability, such as by incorporation of tritiated thymidine or non-radioactive assays, such as MTT assays and the like.
  • Th1 cytokines such as IFN- ⁇ , IL-12, IL-2, and TNF- ⁇
  • Type 2 cytokines such as IL-4, IL-5, IL-9, IL-10, and IL-13.
  • Antigen refers to an immunogenic molecule that provokes an immune response. This immune response may involve antibody production, activation of specific immunologically-competent cells (e.g., T cells), or both.
  • An antigen immunologically-competent cells
  • An antigen immunologically-competent cell
  • An antigen may be, for example, a peptide, glycopeptide, polypeptide, glycopolypeptide, polynucleotide, polysaccharide, lipid or the like. It is readily apparent that an antigen can be synthesized, produced recombinantly, or derived from a biological sample. Exemplary biological samples that can contain one or more antigens include tissue samples, tumor samples, cells, biological fluids, or combinations thereof. Antigens can be chemically synthesized or produced by cells that have been modified or genetically engineered to express an antigen.
  • epitope includes any molecule, structure, amino acid sequence or protein determinant that is recognized and specifically bound by a cognate binding molecule, such as an immunoglobulin, T cell receptor (TCR), chimeric antigen receptor, or other binding molecule, domain or protein.
  • a cognate binding molecule such as an immunoglobulin, T cell receptor (TCR), chimeric antigen receptor, or other binding molecule, domain or protein.
  • Epitopic determinants generally contain chemically active surface groupings of molecules, such as amino acids or sugar side chains, and can have specific three dimensional structural characteristics, as well as specific charge characteristics.
  • Msln 20-28 and “Msln 20-28 peptide,” and “Msln20 peptide” as used herein, refer to a peptide comprising or consisting of mesothelin amino acids 20-28 of SEQ ID NO:50 (human mesothelin, isoform 1); i.e., SLLFLLFSL (SEQ ID NO:31), which peptide can associate with HLA-A*201.
  • Msln 530-538 and Msln 530-538 peptide refer to a peptide comprising or consisting of mesothelin amino acids 530-538 of SEQ ID NO:50; e.g., VLPLTVAEV (SEQ ID NO:32), which peptide can associate with HLA-A*201.
  • Msln 20-28 -specific binding protein refers to a protein or polypeptide that specifically binds to and/or that is specific for and/or that has or confers high avidity for a Msln 20-28 peptide.
  • a protein or polypeptide binds to Msln 20-28 , such as a Msln 20-28 peptide complexed with an MEW or HLA molecule, e.g., on a cell surface, with a, or at least about a, particular affinity.
  • a Msln 20-28 -specific binding protein may bind to a Msln 20-28 peptide, a variant thereof, or a fragment thereof.
  • the Msln 20-28 -specific binding protein may bind to an amino acid sequence of SEQ ID NO:31 (SLLFLLFSL), or an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:31.
  • SLLFLLFSL amino acid sequence of SEQ ID NO:31
  • a Msln 20-28 -specific binding protein binds a Msln 20-28 -peptide:HLA complex (or Msln 20-28 -derived peptide:MHC complex) with an affinity that is about the same as, at least about the same as, or is greater than at or about the affinity exhibited by an exemplary Msln 20-28 -specific binding protein provided herein, such as any of the Msln 20-28 -specific TCRs provided herein, for example, as measured by the same assay.
  • a Msln 20-28 -specific binding protein can bind to an Msln 20-28 epitope as provided herein; e.g., a consensus epitope sequence according to SEQ ID NO:60.
  • a Msln-specific binding protein does not bind, or does not substantially bind, to a non-Msln human protein or peptide having high sequence homology or identity to SEQ ID NO:60.
  • Msln 530-538 -specific binding protein refers to a protein or polypeptide that specifically binds to and/or that is specific for and/or that has or confers high avidity for a Msln 530-538 peptide.
  • a protein or polypeptide binds to Msln 530-538 , such as a Msln 530-538 peptide is complexed with an MEW or HLA molecule, e.g., on a cell surface, with a, or at least about a, particular affinity.
  • a Msln 530-538 -specific binding protein may bind to a Msln 530-538 peptide, a variant thereof, or a fragment thereof.
  • the Msln 530-538 -specific binding protein may bind to an amino acid sequence of SEQ ID NO:32 (VLPLTVAEV), or an amino acid sequence having at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO:32.
  • a Msln 530-538 -specific binding protein binds a Msln 530-538 -peptide:HLA complex (or Msln 530-538 -derived peptide:MHC complex) with an affinity that is about the same as, at least about the same as, or is greater than at or about the affinity exhibited by an exemplary Msln 530-538 specific binding protein provided herein, such as any of the Msln 530-538 -specific TCRs provided herein, for example, as measured by the same assay.
  • a Msln 530-538 -specific binding protein can bind to an Msln 530-538 epitope as provided herein; e.g., a consensus epitope sequence according to SEQ ID NO:61 or 62.
  • a Msln-specific binding protein does not bind, or does not substantially bind, to a non-Msln human protein or peptide having high sequence homology or identity to SEQ ID NO:61 or 62.
  • target molecule which is specifically bound by a binding domain of the present disclosure, may be found on or in association with a cell of interest (“target cell”).
  • target cells include a cancer cell, a cell associated with an autoimmune disease or disorder or with an inflammatory disease or disorder, and an infectious organism or cell (e.g., bacteria, virus, or virus-infected cell).
  • an infectious organism or cell e.g., bacteria, virus, or virus-infected cell.
  • a cell of an infectious organism such as a mammalian parasite, is also contemplated as a target cell.
  • the term “functional avidity” refers to a biological measure or activation threshold of an in vitro immune cell (e.g., T cell, NK cell, NK-T cell) response to a given concentration of a ligand, wherein the biological measures can include cytokine production (e.g., IFN ⁇ production, IL-2 production, etc.), cytotoxic activity, and proliferation.
  • cytokine production e.g., IFN ⁇ production, IL-2 production, etc.
  • T cells that biologically (immunologically) respond in vitro to a low antigen dose by producing cytokines, being cytotoxic, or proliferating are considered to have high functional avidity, while T cells having lower functional avidity require higher amounts of antigen before an immune response, similar to the high-avidity T cells, is elicited.
  • affinity and avidity refers to the strength of any given bond between a binding protein and its antigen/ligand. Some binding proteins are multivalent and bind to multiple antigens—in this case, the strength of the overall connection is the avidity.
  • T cell functions e.g., proliferation, cytokines production, etc.
  • thresholds see, e.g., Betts et al., J. Immunol. 172:6407, 2004; Langenkamp et al., Eur. J. Immunol. 32:2046, 2002.
  • Factors that affect functional avidity include (a) the affinity of a TCR for the pMHC-complex, that is, the strength of the interaction between the TCR and pMHC (Cawthon et al., J. Immunol.
  • the concentration of antigen needed to induce a half-maximum response between the baseline and maximum response after a specified exposure time is referred to as the “half maximal effective concentration” or “EC50”.
  • the EC50 value is generally presented as a molar (moles/liter) amount, but it is often converted into a logarithmic value as follows—log 10(EC50). For example, if the EC50 equals 1 ⁇ M (10 ⁇ 6 M), the log 10 (EC50) value is ⁇ 6. Another value used is pEC50, which is defined as the negative logarithm of the EC50 ( ⁇ log 10 (EC50)). In the above example, the EC50 equaling 1 ⁇ M has a pEC50 value of 6.
  • the functional avidity of the binding proteins of this disclosure will be a measure of its ability to promote IFN ⁇ production by T cells, which can be measured using assays described herein.
  • “High functional avidity” TCRs or binding domains thereof refer to those TCRs or binding domains thereof having a EC50 of at least 10 ⁇ 4 M, at least about 10 ⁇ 5 M, or at least about 10 ⁇ 6 M.
  • mesothelin-specific binding proteins or domains as described herein may expressed by a host T cell and can be functionally characterized according to any of a large number of art accepted methodologies for assaying T cell activity, including determination of T cell binding, activation or induction and also including determination of T cell responses that are antigen-specific.
  • the binding protein is capable of promoting an antigen-specific T cell response against human mesothelin in a class I HLA-restricted manner.
  • the class I HLA-restricted response is transporter-associated with antigen processing (TAP)-independent.
  • the antigen-specific T cell response comprises at least one of a CD4+ helper T lymphocyte (Th) response and a CD8+ cytotoxic T lymphocyte (CTL) response.
  • the CTL response is directed against a mesothelin-overexpressing cell.
  • methodologies for assaying T cell activity include determination of T cell proliferation, T cell cytokine release, antigen-specific T cell stimulation, MHC restricted T cell stimulation, CTL activity (e.g., by detecting 51 Cr release from pre-loaded target cells), changes in T cell phenotypic marker expression, and other measures of T-cell functions.
  • an “immune system cell” refers to any cell of the immune system that originates from a hematopoietic stem cell in the bone marrow, which gives rise to two major lineages, a myeloid progenitor cell (which gives rise to myeloid cells such as monocytes, macrophages, dendritic cells, megakaryocytes, and granulocytes) and a lymphoid progenitor cell (which gives rise to lymphoid cells such as T cells, B cells, and natural killer (NK) cells).
  • myeloid progenitor cell which gives rise to myeloid cells such as monocytes, macrophages, dendritic cells, megakaryocytes, and granulocytes
  • lymphoid progenitor cell which gives rise to lymphoid cells such as T cells, B cells, and natural killer (NK) cells.
  • Exemplary immune system cells include a CD4+ T cell, a CD8+ T cell, a CD4 ⁇ CD8 ⁇ double negative T cell, a ⁇ T cell, a regulatory T cell, a stem cell memory T cell, a natural killer cell (e.g., a NK cell or a NK-T cell), a B cell, and a dendritic cell.
  • Macrophages and dendritic cells may be referred to as “antigen presenting cells” or “APCs,” which are specialized cells that can activate T cells when a major histocompatibility complex (MHC) receptor on the surface of the APC complexed with a peptide interacts with a TCR on the surface of a T cell.
  • MHC major histocompatibility complex
  • T cell or “T lymphocyte” is an immune system cell that matures in the thymus and produces TCRs.
  • T cells can be na ⁇ ve (not exposed to antigen; increased expression of CD62L, CCR7, CD28, CD3, CD127, and CD45RA, and decreased expression of CD45RO as compared to TC M ), memory T cells (T M ) (antigen-experienced and long-lived), and effector cells (antigen-experienced, cytotoxic).
  • T M can be further divided into subsets of central memory T cells (T CM , increased expression of CD62L, CCR7, CD28, CD127, CD45RO, and CD95, and decreased expression of CD54RA as compared to na ⁇ ve T cells) and effector memory T cells (TEM, decreased expression of CD62L, CCR7, CD28, CD45RA, and increased expression of CD127 as compared to na ⁇ ve T cells or TC M ).
  • T CM central memory T cells
  • TEM effector memory T cells
  • Effector T cells refer to antigen-experienced CD8+ cytotoxic T lymphocytes that have decreased expression of CD62L, CCR7, CD28, and are positive for granzyme and perforin as compared to T CM .
  • Other exemplary T cells include regulatory T cells, such as CD4+ CD25+ (Foxp3+) regulatory T cells and Treg17 cells, as well as Tr1, Th3, CD8+CD28-, and Qa-1 restricted T cells.
  • Helper T cells are CD4+ cells that influence the activity of other immune cells by releasing cytokines.
  • CD4+ T cells can activate and suppress an adaptive immune response, and which of those two functions is induced will depend on presence of other cells and signals.
  • T cells can be collected using known techniques, and the various subpopulations or combinations thereof can be enriched or depleted by known techniques, such as by affinity binding to antibodies, flow cytometry, or immunomagnetic selection.
  • Cells of T cell lineage refer to cells that show at least one phenotypic characteristic of a T cell, or a precursor or progenitor thereof that distinguishes the cells from other lymphoid cells, and cells of the erythroid or myeloid lineages.
  • Such phenotypic characteristics can include expression of one or more proteins specific for T cells (e.g., CD3 + , CD4 + , CD8 + ), or a physiological, morphological, functional, or immunological feature specific for a T cell.
  • cells of the T cell lineage may be progenitor or precursor cells committed to the T cell lineage; CD25 + immature and inactivated T cells; cells that have undergone CD4 or CD8 linage commitment; thymocyte progenitor cells that are CD4 + CD8 + double positive; single positive CD4 + or CD8 + ; TCR ⁇ or TCR ⁇ ; or mature and functional or activated T cells.
  • a “hematopoietic progenitor cell” is a cell derived from hematopoietic stem cells (HSCs) or fetal tissue that is capable of further differentiation into mature cell types (e.g., cells of the T cell lineage).
  • HSCs hematopoietic stem cells
  • CD24 lo Lin ⁇ CD117 + hematopoietic progenitor cells are useful.
  • hematopoietic progenitor cells may include embryonic stem cells, which are capable of further differentiation to cells of the T cell lineage.
  • Hematopoietic progenitor cells may be from various animal species, including human, mouse, rat, or other mammals.
  • a “thymocyte progenitor cell” or “thymocyte” is a hematopoietic progenitor cell present in the thymus.
  • Hematopoietic stem cells or “HSCs” refer to undifferentiated hematopoietic cells that are capable of self-renewal either in vivo, essentially unlimited propagation in vitro, and capable of differentiation to other cell types including cells of the T cell lineage. HSCs may be isolated, for example, but not limited to, from fetal liver, bone marrow, and cord blood.
  • Embryonic stem cells refer to undifferentiated embryonic stem cells that have the ability to integrate into and become part of the germ line of a developing embryo. Embryonic stem cells are capable of differentiating into hematopoietic progenitor cells and any tissue or organ. Embryonic stem cells that are suitable for use herein include cells from the J1 ES cell line, 129J ES cell line, murine stem cell line D3 (American Type Culture Collection), the R1 or E14K cell lines derived from 129/Sv mice, cell lines derived from Balb/c and C57Bl/6 mice, and human embryonic stem cells (e.g., from WICELL® Research Institute, WI; or ES cell International, Melbourne, Australia).
  • T cell receptor refers to an immunoglobulin superfamily member (having a variable binding domain, a constant domain, a transmembrane region, and a short cytoplasmic tail; see, e.g., Janeway, et al., Immunobiology: The Immune System in Health and Disease, 3 rd Ed., Current Biology Publications, p. 4:33, 1997) capable of specifically binding to an antigen peptide bound to a MHC receptor.
  • a TCR can be found on the surface of a cell or in soluble form and generally is comprised of a heterodimer having ⁇ and ⁇ chains (also known as TCR ⁇ and TCR ⁇ , respectively), or ⁇ and ⁇ chains (also known as TCR ⁇ and TCR ⁇ , respectively).
  • TCR chains e.g., ⁇ -chain and ⁇ -chain
  • the extracellular portion of TCR chains e.g., ⁇ -chain and ⁇ -chain
  • a variable domain e.g., ⁇ -chain variable domain or V ⁇
  • ⁇ -chain variable domain or V ⁇ typically amino acids 1 to 116 based on Kabat numbering (Kabat, et al., “Sequences of Proteins of Immunological Interest,” US Dept.
  • variable domains contain complementary determining regions (CDRs) separated by framework regions (FRs) (see, e.g., Jores, et al., Proc. Nat'l Acad. Sci. U.S.A. 57:9138, 1990; Chothia, et al., EMBO J.
  • CDRs complementary determining regions
  • FRs framework regions
  • a TCR is found on the surface of T cells (or T lymphocytes) and associates with the CD3 complex.
  • the source of a TCR as used in the present disclosure may be from various animal species, such as a human, mouse, rat, cat, dog, goat, horse, or other mammal.
  • CD3 is a multi-protein complex of six chains (see, Borst J, et al., J Biol Chem, 258(8):5135-41, 1983 and Janeway, et al., p. 172 and 178, 1999 supra).
  • the complex includes a CD3 ⁇ chain, a CD3 ⁇ chain, two CD3 ⁇ chains, and a homodimer of CD3 ⁇ chains.
  • the CD3 ⁇ , CD3 ⁇ , and CD3 ⁇ chains are related cell surface proteins of the immunoglobulin superfamily containing a single immunoglobulin domain.
  • the transmembrane regions of the CD3 ⁇ , CD3 ⁇ , and CD3 ⁇ chains are negatively charged, which is a characteristic that is thought to allow these chains to associate with positively charged regions of TCR chains.
  • CD3 ⁇ , CD3 ⁇ , and CD3 ⁇ chains each contain a single conserved motif known as an immunoreceptor tyrosine-based activation motif or ITAM, whereas each CD3 ⁇ chain has three. Without being bound by any one theory, it is believed the ITAMs are important for the signaling capacity of a TCR complex.
  • CD3 as used in the present disclosure may be from various animal species, including human, mouse, rat, or other mammals.
  • TCR complex refers to a complex formed by the association of CD3 with TCR.
  • a TCR complex can be composed of a CD3 ⁇ chain, a CD3 ⁇ chain, two CD3 ⁇ chains, a homodimer of CD3 ⁇ chains, a TCR ⁇ chain, and a TCR ⁇ chain.
  • a TCR complex can be composed of a CD3 ⁇ chain, a CD3 ⁇ chain, two CD3 ⁇ chains, a homodimer of CD3 ⁇ chains, a TCR ⁇ chain, and a TCR chain.
  • a “component of a TCR complex,” as used herein, refers to a TCR chain (i.e., TCR ⁇ , TCR ⁇ , TCR ⁇ , or TCR ⁇ ), a CD3 chain (i.e., CD3 ⁇ , CD3 ⁇ , CD3 ⁇ , or CD3 ⁇ ), or a complex formed by two or more TCR chains or CD3 chains (e.g., a complex of TCR ⁇ and TCR ⁇ , a complex of TCR ⁇ and TCR ⁇ , a complex of CD3 ⁇ and CD3 ⁇ , a complex of CD3 ⁇ and CD3 ⁇ , or a sub-TCR complex of TCR ⁇ , TCR ⁇ , CD3 ⁇ , CD3 ⁇ , and two CD3 ⁇ chains).
  • MHC Major histocompatibility complex
  • HLA human leukocyte antigen
  • binding proteins that are capable of specifically binding to a mesothelin peptide antigen as described herein (e.g., a peptide comprising, consisting, or consisting essentially of the amino acid sequence set forth in SEQ ID NO:31 or SEQ ID NO:32).
  • Binding proteins herein include a TCR alpha chain variable domain (V ⁇ ) and a TCR beta chain variable domain (V ⁇ ).
  • a mesothelin-specific binding protein is capable of specifically binding to a mesothelin peptide:HLA complex, such as a mesothelin peptide:HLA-A*02:01 complex.
  • a Msln- 530-538 -specific binding protein comprises: (a) a TCR V ⁇ comprising a CDR3 amino acid sequence as set forth in SEQ ID NO:37 or 39, and a TCR V ⁇ , wherein the TCR V ⁇ optionally comprises an amino acid sequence having at least about 85% (i.e., at least about 86%, 85%, 88%, 89% 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more) identity to the amino acid sequence set forth in SEQ ID NO:99 or 101; (b) a TCR V ⁇ comprising a CDR3 amino acid sequence as set forth in SEQ ID NO:38 or 40, and (b) a TCR V ⁇ , wherein the TCR V ⁇ optionally comprises an amino acid sequence having at least about 85% (i.e., at least about 86%, 85%, 88%, 89% 90%, 91%, 92%, 93%, 94%, 95%
  • an encoded polypeptide of this disclosure can comprise a “signal peptide” (also known as a leader sequence, leader peptide, or transit peptide).
  • Signal peptides target newly synthesized polypeptides to an appropriate location inside or outside the cell.
  • a signal peptide may be removed from the polypeptide during or once localization or secretion is completed.
  • Polypeptides that have a signal peptide are referred to herein as a “pre-protein” and polypeptides having their signal peptide removed are referred to herein as “mature” proteins or polypeptides.
  • Representative signal peptides include those amino acid sequences from position 1 to position 19 any one of SEQ ID NOs: 6, 14, 22, 28, or 29; from position 1 to 17 of SEQ ID NO: 7; from position 1 to 22 of SEQ ID NO: 15; from position 1 to 21 of SEQ ID NO: 23.
  • Exemplary mature polypeptide sequences are provided in SEQ ID NOs:95-119.
  • a Msln 530-538 -specific binding protein can comprise a TCR V ⁇ comprising an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:100 or 102 and/or a TCR V ⁇ comprising an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:99 or 101.
  • a binding protein comprises a variant of a referenced TCR variable domain sequence, provided that at least three or four of the CDRs of the binding protein have no change in sequence according to a referenced TCR variable domain sequence, wherein the CDRs that do have sequence changes have only up to two amino acid substitutions, up to a contiguous five amino acid deletion, or a combination thereof.
  • a Msln 530-538 -specific binding protein comprises a CDR3 ⁇ amino acid sequence as set forth in SEQ ID NO:39 and a CDR3 ⁇ amino acid sequence as set forth in SEQ ID NO:40.
  • the binding protein further comprises a CDR1 ⁇ amino acid sequence as set forth SEQ ID NO:93, a CDR2 ⁇ amino acid sequence as set forth in SEQ ID NO:94, a CDR1 ⁇ amino acid sequence as set forth in any one of SEQ ID NOs: 83, 84, or 91, and/or a CDR2 ⁇ amino acid sequence as set forth in SEQ ID NO:92.
  • the V ⁇ comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:102, and/or the V ⁇ comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:101, wherein there are optionally no changes in CDR1 ⁇ , CDR2 ⁇ , CDR1 ⁇ , and/or CDR2 ⁇ .
  • the Msln 530-538 -specific binding protein comprises a TCR V ⁇ comprising an amino acid sequence having at least about 85% identity to an amino acid sequence encoded by TRBJ2-3*01 (e.g., to a TRBJ2-3*01-encoded amino acid sequence that is at least about 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 15 contiguous amino acids in length), and/or an amino acid sequence having at least about 85% identity to an amino acid sequence encoded by TRAV21*01 or TRAV21*02 (e.g., to a TRAV21*01 or TRAV21*02-encoded sequence that is at least about 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, or 107 amino acids in length), and/or an amino acid sequence having at least about 85% identity to an amino acid sequence encoded by TRBV5-4*01 (e.g., to a TRBV5
  • a Msln 530-538 -specific binding protein comprises a TCR V ⁇ comprising or consisting of the amino acid sequence set forth in SEQ ID NO:102 and a TCR V ⁇ comprising or consisting of the amino acid sequence set forth in SEQ ID NO:101.
  • a Msln 530-538 -specific binding protein comprises a CDR3 ⁇ amino acid sequence as set forth in SEQ ID NO:37 and a CDR3 ⁇ amino acid sequence as set forth in SEQ ID NO:38.
  • the binding protein further comprises a CDR1 ⁇ amino acid sequence as set forth SEQ ID NO:89, a CDR2 ⁇ amino acid sequence as set forth in SEQ ID NO:90, a CDR1 ⁇ amino acid sequence as set forth in any one of SEQ ID NOs: 83 or 87, and a CDR2 ⁇ amino acid sequence as set forth in SEQ ID NO:88.
  • the V ⁇ comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:100, and/or the V ⁇ comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:99, wherein there are optionally no changes in CDR1 ⁇ , CDR2 ⁇ , CDR1 ⁇ , and/or CDR2 ⁇ .
  • a Msln 530-538 -specific binding protein comprises an amino acid sequence having at least about 85% identity to an amino acid sequence encoded by TRAV4-1*01 (e.g., to a TRAV4-1*01-encoded sequence that is at least about 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, or 108 amino acids in length), and/or an amino acid sequence having at least about 85% identity to an amino acid sequence encoded by TRAJ18*01 (e.g., to a TRAJ18*01-encoded sequence that is at least about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 amino acids in length) and/or an amino acid sequence having at least about 85% identity to an amino acid sequence encoded by TRBJ1-1*01 (e.g., to a TRBJ1-1*01-encoded sequence that is at least about 5, 6, 7, 8, 9, 10, 11,
  • a Msln 530-538 -specific binding protein comprises a TCR V ⁇ comprising or consisting of the amino acid sequence set forth in SEQ ID NO:100 and a TCR V ⁇ comprising or consisting of the amino acid sequence set forth in SEQ ID NO:99.
  • alanine mutagenesis of any one or more of residues 3, 5, 6, or 9 of SEQ ID NO:32 does not abrogate or does not substantially impair binding by a Msln 530-538 -specific binding protein.
  • a Msln 530-538 -specific binding protein is capable of binding to a peptide comprising or consisting of the consensus amino acid sequence set forth in SEQ ID NO:61; e.g., in a peptide:HLA complex as disclosed herein.
  • alanine mutagenesis of any one or more of residues 1, 5, or 9 of SEQ ID NO:32 does not abrogate or does not substantially impair binding by a Msln 530-538 -specific binding protein.
  • a Msln 530-538 -specific binding protein is capable of binding to a peptide comprising or consisting of the consensus amino acid sequence set forth in SEQ ID NO:62; e.g., in a peptide:HLA complex as disclosed herein.
  • Msln-specific binding proteins advantageously present low to no risk of alloreactivity against non-Msln targets; e.g., that are expressed in healthy tissue.
  • the present disclosure shows that Msln-specific binding proteins do not react, or do not substantially react, with human proteins with sequence homology to a Msln peptide antigen as provided herein.
  • the binding proteins are highly specific for Msln peptide antigens.
  • a Msln 530-538 -specific binding protein of the present disclosure does not bind, or does not specifically bind relative to binding to Msln 530-538 , to a peptide:HLA complex wherein the peptide comprises or consists of the amino acid sequence set forth in any one or more of SEQ ID NOs:63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, and 77, and wherein the HLA optionally comprises an HLA-A2, such as HLA-A:02*01.
  • a Msln 20-28 -specific binding protein comprises: (a) a TCR V ⁇ comprising a CDR3 amino acid sequence as set forth in SEQ ID NO:33 or 35, and a TCR V ⁇ , wherein the TCR V ⁇ optionally has at least about 85% (i.e., at least about 85%, 86%, 87%, 88%, 89% 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more) identity to the amino acid sequence set forth in SEQ ID NO:95 or 97; (b) a TCR V ⁇ comprising a CDR3 amino acid sequence as set forth in SEQ ID NO:34 or 36, and (b) a TCR V ⁇ , wherein the TCR V ⁇ optionally has at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:96 or 98; or (c) a TCR V ⁇ comprising a CDR3 amino acid sequence as set forth in SEQ ID NO:
  • a Msln 20-28 -specific binding protein can comprise a TCR V ⁇ comprising an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:96 or 98 and/or a TCR V ⁇ comprising an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:95 or 97.
  • a binding protein comprises a variant of a referenced TCR variable domain sequence, provided that at least three or four of the CDRs of the binding protein have no change in sequence according to a referenced TCR variable domain sequence, wherein the CDRs that do have sequence changes have only up to two amino acid substitutions, up to a contiguous five amino acid deletion, or a combination thereof.
  • a Msln 20-28 -specific binding protein specific binding protein comprises a CDR3 ⁇ amino acid sequence as set forth in SEQ ID NO:33 and a CDR3 ⁇ amino acid sequence as set forth in SEQ ID NO:34.
  • the binding protein further comprises a CDR1 ⁇ amino acid sequence as set forth SEQ ID NO:80, a CDR2 ⁇ amino acid sequence as set forth in SEQ ID NO:81 or 118, a CDR1 ⁇ amino acid sequence as set forth in any one of SEQ ID NOs: 78, 83, or 84, and a CDR2 ⁇ amino acid sequence as set forth in SEQ ID NO:79.
  • the V ⁇ comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:96, and/or the V ⁇ comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:95, wherein there are optionally no changes in CDR1 ⁇ , CDR2 ⁇ , CDR1 ⁇ , and/or CDR2 ⁇ .
  • the Msln 20-28 -specific binding protein comprises (i) a TCR V ⁇ comprising (a) an amino acid sequence having at least about 85% identity (i.e., at least about 85%, 86%, 87%, 88%, 89% 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more) to an amino acid sequence encoded by TRBV12-4*01 (e.g., to a TRBV12-4*01-encoded amino acid sequence that is at least about 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, or 108 contiguous amino acids in length); and/or (b) an amino acid sequence having at least about 85% identity an amino acid sequence encoded by TRBJ2-7*01 (e.g., to a TRBJ2-7*01-encoded amino acid sequence that is at least about 5, 6, 7, 8, 9, 10, 11, 12, 13,
  • a Msln 20-28 -specific binding protein comprises a TCR V ⁇ comprising or consisting of the amino acid sequence set forth in SEQ ID NO:96, and a TCR V ⁇ comprising or consisting of the amino acid sequence set forth in SEQ ID NO:95.
  • a Msln 20 -28-specific binding protein a CDR3 ⁇ amino acid sequence as set forth in SEQ ID NO:35 and a CDR3 ⁇ amino acid sequence as set forth in SEQ ID NO:36.
  • the binding protein further comprises a CDR1 ⁇ amino acid sequence as set forth SEQ ID NO:85, a CDR2 ⁇ amino acid sequence as set forth in SEQ ID NO:86 or 119, a CDR1 ⁇ amino acid sequence as set forth in any one of SEQ ID NOs:82, 83, or 84, and a CDR2 ⁇ amino acid sequence as set forth in SEQ ID NO:79.
  • the V ⁇ comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:98, and/or the V ⁇ comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:97, wherein there are optionally no changes in CDR1 ⁇ , CDR2 ⁇ , CDR1 ⁇ , and/or CDR2 ⁇ .
  • the Msln 20-28 -specific binding protein comprises a TCR V ⁇ comprising (a) an amino acid sequence having at least about 85% identity to an amino acid sequence encoded by TRAV12-3*01 (e.g., to a TRAV12-3*01-encoded amino acid sequence that is at least about 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, or 108 contiguous amino acids in length) and/or (b) an amino acid sequence having at least about 85% identity to an amino acid sequence encoded by TRAJ29*01 (e.g., to a TRAJ29*01-encoded amino acid sequence that is at least about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 amino acids long), and/or (c) and/or an amino acid sequence having at least about 85% identity to an amino acid sequence encoded by TRBJ2-3*01 (e.g., to a TRB
  • a Msln 20-28 -specific binding protein comprises a TCR V ⁇ comprising or consisting of the amino acid sequence set forth in SEQ ID NO:98 and a TCR V ⁇ comprising or consisting of the amino acid sequence set forth in SEQ ID NO:97.
  • alanine mutagenesis of any one or more of residues 1, 2, 7, 8, or 9 of SEQ ID NO:31 does not abrogate or does not substantially impair binding by a Msln 20-28 -specific binding protein.
  • a Msln 20-28 -specific binding protein is capable of binding to a peptide comprising or consisting of the consensus amino acid sequence set forth in SEQ ID NO:60; e.g., in a peptide:HLA complex as disclosed herein.
  • a Msln-specific binding protein is capable of binding to a Msln peptide:HLA complex, wherein the Msln peptide comprises the amino acid sequence set forth in SEQ ID NO:31 or 32 and wherein the HLA is or comprises HLA-A2, such as HLA-A*02:01.
  • an immune cell e.g., a T cell
  • a Msln-specific binding protein of this disclosure does not produce IFN- ⁇ and/or does not exhibit activation (e.g., CD8 expression, CD3 expression, Nur77 expression) and/or cytotoxic activity (e.g., specific killing, production and release of a perforin and/or a granzyme) when contacted with a cell expressing: (i) HLA-C6:02:01; (ii) HLA-B13:01:01 without HLA-B13:02:01; (iii) HLA-A3; (iv) HLA-A29; (v) HLA-B40; (vi) HLA-B44; (vii) HLA-C3; (viii) HLA-C16; (ix) HLA-A1; (x) HLA-24; (xi) HLA-B7; (xii) HLA-B57; (xiii)
  • a Msln-specific binding protein when expressed on the surface of a host cell, is capable of binding to a Msln peptide:HLA complex as disclosed herein in the absence of, or independent of, CD8.
  • a binding protein according to the present disclosure has a Msln peptide EC50 of about 9 ⁇ M, about 8 ⁇ M, about 7 ⁇ M, about 6 ⁇ M, about 5 ⁇ M, about 4 ⁇ M, about 3 ⁇ M, about 2 ⁇ M, about 1 ⁇ M, about 0.9 ⁇ M, about 0.8 ⁇ M, about 0.7 ⁇ M, about 0.6 ⁇ M, about 0.5 ⁇ M, about 0.4 ⁇ M, about 0.3 ⁇ M, about 0.2 ⁇ M, or less.
  • a Msln-specific binding protein is capable of more efficiently associating with a CD3 protein, and/or has increased expression at a cell surface relative to an endogenous TCR, when the Msln-specific binding protein is expressed in a host T cell or NK-T cell.
  • the binding protein is a TCR, a single chain TCR (scTCR), or a CAR.
  • the binding protein is a TCR.
  • the binding protein comprises a TCR V ⁇ , a TCR CP, a TCR V ⁇ , and a TCR C ⁇ , wherein the V ⁇ and the C ⁇ together comprise a TCR ⁇ chain (TCR ⁇ ), and wherein the V ⁇ and the C ⁇ together comprise a TCR ⁇ chain (TCR ⁇ ), and wherein the TCR ⁇ and the TCR ⁇ are capable of associating to form a dimer.
  • a TCR C ⁇ comprises a cysteine amino acid in place of a native serine at amino acid position 57 (e.g., GV(S ⁇ C)TD) and a TCR C ⁇ comprises a cysteine amino acid in place of a native threonine at amino acid position 48 (e.g., DK(T ⁇ C)VL; see. e.g., Cohen et al., Cancer Res. 67(8):3898-3903 (2007)).
  • a Msln-specific binding protein is a TCR comprising a TCR ⁇ and a TCR ⁇ , wherein the TCR ⁇ and the TCR ⁇ respectively comprise an amino acid sequence having at least about 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identity, or more, to the amino acid sequences set forth in SEQ ID NOs: (i) 103 or 6 (TCR ⁇ ) and 104 or 7 (TCR ⁇ ); (ii) 105 or 14 (TCR ⁇ ) and 106 or 15 (TCR ⁇ ); (iii) 107 or 22 (TCR ⁇ ) and 108 or 23 (TCR ⁇ ); or (iv) 109 or 28 (TCR ⁇ ) and 110 or 29 (TCR ⁇ ).
  • the binding protein is a soluble TCR, optionally including or coupled to a cytotoxic and/or detectable element or agent.
  • a cytotoxic and/or detectable element or agent see, e.g., Walseng et al., PLoS One doi:10.1371/journal.pone.0119559 (2015).
  • Methods useful for isolating and purifying recombinantly produced soluble TCR may include obtaining supernatants from suitable host cell/vector systems that secrete the recombinant soluble TCR into culture media and then concentrating the media using a commercially available filter. Following concentration, the concentrate may be applied to a single suitable purification matrix or to a series of suitable matrices, such as an affinity matrix or an ion exchange resin.
  • One or more reverse phase HPLC steps may be employed to further purify a recombinant polypeptide. These purification methods may also be employed when isolating an immunogen from its natural environment. Methods for large scale production of one or more of the isolated/recombinant soluble TCR described herein include batch cell culture, which is monitored and controlled to maintain appropriate culture conditions. Purification of the soluble TCR may be performed according to methods described herein and known in the art and that comport with laws and guidelines of domestic and foreign regulatory agencies.
  • two or more distinct polypeptide domains or sequences are connected by a linker (e.g., a TCRV ⁇ and a TCRV ⁇ in the context of a scTCR or a CAR).
  • a “linker” refers to an amino acid sequence that connects two proteins, polypeptides, peptides, domains, regions, or motifs and may provide a spacer function compatible with interaction of the two sub-binding domains so that the resulting polypeptide retains a specific binding affinity (e.g., scTCR) to a target molecule or retains signaling activity (e.g., TCR complex).
  • a linker is comprised of about two to about 35 amino acids, about four to about 20 amino acids, about eight to about 15 amino acids, about 15 to about 25 amino acids, or another suitable number of amino acids.
  • a linker is preferably chemically inert, flexible, and non-immunogenic or minimally immunogenic. Linker sequences can be repeated so as to achieve a desired length to, for example, facilitate a desired protein interaction by or between linked domains.
  • Exemplary linkers (including glycine-serine linkers) and properties of linkers are discussed in, for example, Chen et al., Adv. Drug Deliv Rev, 65(10):1357-1369 (2013), and in van Rosmalen et al., Biochemistry 56(60):6565-6574 (2017), which linker amino acid sequences and design properties are incorporated herein by reference.
  • a Msln-specific binding protein is or comprises a scTCR (e.g., single chain ⁇ TCR proteins such as V ⁇ -L-V ⁇ , V ⁇ -L-V ⁇ , V ⁇ -C ⁇ -L-V ⁇ , or V ⁇ -L-V ⁇ -C ⁇ , wherein V ⁇ and V ⁇ are TCR ⁇ and ⁇ variable domains respectively, C ⁇ and C ⁇ are TCR ⁇ and ⁇ constant domains, respectively, and L is a linker).
  • scTCR e.g., single chain ⁇ TCR proteins such as V ⁇ -L-V ⁇ , V ⁇ -L-V ⁇ , V ⁇ -C ⁇ -L-V ⁇ , or V ⁇ -L-V ⁇ -C ⁇ , wherein V ⁇ and V ⁇ are TCR ⁇ and ⁇ variable domains respectively, C ⁇ and C ⁇ are TCR ⁇ and ⁇ constant domains, respectively, and L is a linker).
  • a Msln-specific binding protein is or comprises a CAR.
  • CAR Chimeric antigen receptor
  • fusion protein of the present disclosure engineered to contain two or more naturally occurring (or engineered) amino acid sequences linked together in a way that does not occur naturally or does not occur naturally in a host cell, which fusion protein can function as a receptor when present on a surface of a cell.
  • CARs of the present disclosure include an extracellular portion comprising an antigen-binding domain (e.g., obtained or derived from an immunoglobulin or immunoglobulin-like molecule, such as a scFv or scTCR derived from an antibody or TCR specific for a cancer antigen, or an antigen-binding domain derived or obtained from a killer immunoreceptor from an NK cell, or from another protein (natural, recombinant, or synthetic) that has, or is engineered to possess, the ability to specifically bind to an antigen) linked to a transmembrane domain and one or more intracellular signaling domains (optionally containing co-stimulatory domain(s)) (see, e.g., Sadelain et al., Cancer Discov., 3(4):388 (2013); see also Harris and Kranz, Trends Pharmacol.
  • an antigen-binding domain e.g., obtained or derived from an immunoglobulin or immunoglobulin-like molecule
  • a binding protein comprises a CAR comprising an antigen-specific TCR binding domain (see, e.g., Walseng et al., Scientific Reports 7:10713, 2017; the TCR CAR constructs and methods of which are hereby incorporated by reference in their entirety).
  • polynucleotides that encode a Msln-specific binding protein, or a portion thereof, (e.g., TCR variable domain) of this disclosure. It will be appreciated by those of ordinary skill in the art that, due to the degeneracy of the genetic code, there are numerous nucleotide sequences that encode a binding protein or portion thereof, as described herein. Some such polynucleotides can bear limited or minimal sequence identity to the nucleotide sequence of a native, original, or identified polynucleotide sequence. Nonetheless, polynucleotides that vary due to differences in codon usage are expressly contemplated by the present disclosure.
  • sequences that have been codon-optimized for expression in a host cell are specifically contemplated. Codon optimization can be performed using known techniques and tools, e.g., using the GenScript® OptimumGeneTM tool. Codon-optimized sequences include sequences that are at least partially codon-optimized (i.e., one or more codon is optimized for expression in the host cell) and those that are fully codon-optimized. Codon optimization for expression in certain immune host cells is described in, for example, Scholten et al., Clin. Immunol. 119:135, 2006.
  • a polynucleotide encoding a Msln-specific binding protein comprises a polynucleotide having at least about 50% (i.e., at least about 50%, 55%, 60%, 65% 70%, 75%, 80%, 85%, 86%, 87%, 89% 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more) identity to the polynucleotide sequence set forth in any one of SEQ ID NOs:1-4, 9-12, 17-20, 25, and 26.
  • a TCR ⁇ chain-encoding polynucleotide and a TCR ⁇ chain-encoding polynucleotide are provided that have at least about 50% identity to the polynucleotide sequences set forth in SEQ ID NOs: (i) 1 and 3, respectively; (ii) 2 and 4, respectively; (iii) 9 and 11, respectively; (iv) 10 and 12, respectively; (v) 17 and 19, respectively; (vi) 18 and 20, respectively; or (vii) 25 and 26, respectively.
  • a polynucleotide encoding two or more components or portions of a binding protein or TCR of the present disclosure comprises the two or more coding sequences operatively associated in a single open reading frame.
  • desired gene products such as, for example, contemporaneous expression of alpha and beta chains of a TCR, such that they are produced in about a 1:1 ratio.
  • two or more substituent gene products of a binding protein of this disclosure such as a TCR (e.g., alpha and beta chains), are expressed as separate molecules and associate post-translationally.
  • two or more substituent gene products of a binding protein of this disclosure are expressed as a single peptide with the parts separated by a cleavable or removable segment.
  • self-cleaving peptides are useful for expression of separable polypeptides encoded by a single polynucleotide or vector are known in the art and include, for example, a P2A peptide encoded by a polynucleotide having the nucleotide sequence shown in any one of SEQ ID NOS:41-46, a Thoseaasigna virus 2A (T2A) peptide, such as a peptide encoded by a polynucleotide having the nucleotide sequence shown in SEQ ID NO:47, an Equine rhinitis A virus (ERAV) 2A (E2A) peptide, such as a peptide encoded by a polynucleotide having the nucleotide sequence shown in SEQ ID NO:48, and a Foot-and-Mouth disease virus 2A (F2A) peptide, such as a peptide encode
  • Exemplary polynucleotides encoding a Msln-specific TCR of the present disclosure wherein a polynucleotide encoding a self-cleaving peptide is disposed between a polynucleotide encoding a TCR ⁇ chain and a polynucleotide encoding a TCR ⁇ chain, include those that encode an amino acid sequence as set forth in any one of SEQ ID NOs:8, 16, 24, and 30.
  • Exemplary such polynucleotides have a polynucleotide sequence as set forth in any one of SEQ ID NOs:5, 13, 21, 27, and 120; in certain embodiments, a polynucleotide is provided that has at least about 50% identity to the polynucleotide sequence as set forth in any one of SEQ ID NOs:5, 13, 21, 27, and 120.
  • a binding protein is expressed as part of a transgene construct that encodes, and/or a host immune cell containing the binding-protein-encoding polynucleotide can further encode: one or more additional accessory protein, such as a safety switch protein; a tag, a selection marker; a CD8 co receptor ⁇ chain; a CD8 co-receptor ⁇ chain or both; or any combination thereof.
  • additional accessory protein such as a safety switch protein
  • a tag, a selection marker such as a CD8 co receptor ⁇ chain
  • CD8 co-receptor ⁇ chain or both or any combination thereof.
  • Polynucleotides and transgene constructs useful for encoding and expressing binding proteins and accessory components are described in published PCT application no.
  • WO 2018/058002 the polynucleotides, transgene constructs, and accessory components, including the nucleotide and amino acid sequences thereof, of which are hereby incorporated by reference. It will be understood that any or all of a binding protein of the present disclosure, a safety switch protein, a tag, a selection marker, a CD8 co-receptor ⁇ chain, or a CD8 co-receptor ⁇ -chain may be encoded by a single nucleic acid molecule or may be encoded by polynucleotide sequences that are, or are present on, separate nucleic acid molecules.
  • Exemplary safety switch proteins include, for example, a truncated EGF receptor polypeptide (huEGFRt) that is devoid of extracellular N terminal ligand binding domains and intracellular receptor tyrosine kinase activity, but that retains its native amino acid sequence, has type I transmembrane cell surface localization, and has a conformationally intact binding epitope for pharmaceutical-grade anti-EGFR monoclonal antibody, cetuximab (Erbitux) tEGF receptor (tEGFr; Wang et al., Blood 118:1255-1263, 2011); a caspase polypeptide (e.g., iCasp9; Straathof et al., Blood 105:4247-4254, 2005; Di Stasi et al., N.
  • huEGFRt truncated EGF receptor polypeptide
  • accessory components useful for recombinant host cells of the present disclosure comprise a tag or selection marker that allows the cells to be identified, sorted, isolated, enriched, or tracked.
  • marked cells having desired characteristics e.g., an antigen-specific TCR and a safety switch protein
  • selection marker comprises a nucleic acid construct (and the encoded gene product) that confers an identifiable change to a cell permitting detection and positive selection of immune cells transduced with a polynucleotide comprising a selection marker.
  • RQR is a selection marker that comprises a major extracellular loop of CD20 and two minimal CD34 binding sites.
  • an RQR-encoding polynucleotide comprises a polynucleotide that encodes the 16-amino-acid CD34 minimal epitope.
  • the CD34 minimal epitope is incorporated at the amino terminal position of a CD8 co-receptor stalk domain (Q8).
  • the CD34 minimal binding site sequence can be combined with a target epitope for CD20 to form a compact marker/suicide gene for T cells (RQR8) (Philip et al., 2014, incorporated by reference herein).
  • This construct allows for the selection of immune cells expressing the construct, with for example, CD34 specific antibody bound to magnetic beads (Miltenyi) and that utilizes clinically accepted pharmaceutical antibody, rituximab, that allows for the selective deletion of a transgene expressing engineered T cell (Philip et al., 2014).
  • selection markers also include several truncated type I transmembrane proteins normally not expressed on T cells: the truncated low-affinity nerve growth factor, truncated CD19, and truncated CD34 (see for example, Di Stasi et al., N. Engl. J. Med. 365:1673-1683, 2011; Mavilio et al., Blood 83:1988-1997, 1994; Fehse et al., Mol. Ther. 1:448-456, 2000; each incorporated herein in their entirety).
  • a useful feature of CD19 and CD34 is the availability of the off-the-shelf Miltenyi CliniMACsTM selection system that can target these markers for clinical-grade sorting.
  • CD19 and CD34 are relatively large surface proteins that may tax the vector packaging capacity and transcriptional efficiency of an integrating vector.
  • Surface markers containing the extracellular, non-signaling domains or various proteins e.g., CD19, CD34, LNGFR
  • Any selection marker may be employed and should be acceptable for Good Manufacturing Practices.
  • selection markers are expressed with a polynucleotide that encodes a gene product of interest (e.g., a binding protein of the present disclosure, such as a TCR or CAR).
  • selection markers include, for example, reporters such as GFP, EGFP, ⁇ -gal or chloramphenicol acetyltransferase (CAT).
  • a selection marker such as, for example, CD34 is expressed by a cell and the CD34 can be used to select enrich for, or isolate (e.g., by immunomagnetic selection) the transduced cells of interest for use in the methods described herein.
  • a CD34 marker is distinguished from an anti-CD34 antibody, or, for example, a scFv, TCR, or other antigen recognition moiety that binds to CD34.
  • a selection marker comprises an RQR polypeptide, a truncated low-affinity nerve growth factor (tNGFR), a truncated CD19 (tCD19), a truncated CD34 (tCD34), or any combination thereof.
  • tNGFR truncated low-affinity nerve growth factor
  • tCD19 truncated CD19
  • tCD34 truncated CD34
  • standard techniques may be used for recombinant DNA, peptide, and oligonucleotide synthesis; immunoassays; tissue culture; and transformation (e.g., electroporation and lipofection). Enzymatic reactions and purification techniques may be performed according to manufacturer's specifications or as commonly accomplished in the art or as described herein.
  • vectors that comprise a polynucleotide according to the present disclosure.
  • Any suitable expression vector including an exemplary expression vector as disclosed herein, may be used.
  • the expression vector may be configured to or capable of delivering the polynucleotide to a host cell.
  • a typical vector may include a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked, or which is capable of replication in a host organism.
  • some examples of vectors include plasmids, viral vectors, cosmids, and others.
  • Some vectors may be capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors), whereas other vectors may be integrated into the genome of a host cell upon introduction into the host cell and thereby replicate along with the host genome. Additionally, some vectors are capable of directing the expression of genes to which they are operatively linked (these vectors may be referred to as “expression vectors”).
  • agents e.g., polynucleotides encoding a Msln-specific binding protein, or a variant thereof, as described herein
  • each agent may reside in separate or the same vectors, and multiple vectors (each containing a different agent or the same agent) may be introduced to a cell or cell population or administered to a subject.
  • expression vector refers to a DNA construct containing a nucleic acid molecule that is operably linked to a suitable control sequence capable of effecting the expression of the nucleic acid molecule in a suitable host.
  • control sequences include a promoter to effect transcription, an optional operator sequence to control such transcription, a sequence encoding suitable mRNA ribosome binding sites, and sequences which control termination of transcription and translation.
  • the vector may be a plasmid, a phage particle, a virus, or simply a potential genomic insert. Once transformed into a suitable host, the vector may replicate and function independently of the host genome, or may, in some instances, integrate into the genome itself.
  • plasmid,” “expression plasmid,” “virus” and “vector” are often used interchangeably.
  • a viral vector is used to introduce a non-endogenous nucleic acid sequence encoding a polypeptide specific for a target.
  • a viral vector may be a retroviral vector or a lentiviral vector.
  • a viral vector may also include nucleic acid sequences encoding transduction marker.
  • Viral vectors suitable for use with the compositions of the instant disclosure include those identified for human gene therapy applications (see Pfeifer and Verma, Ann. Rev. Genomics Hum. Genet. 2: 177, 2001).
  • Suitable viral vectors include vectors based on RNA viruses, such as retrovirus-derived vectors, e.g., Moloney murine leukemia virus (MLV)-derived vectors, and include more complex retrovirus-derived vectors, e.g., lentivirus-derived vectors. HIV-1-derived vectors belong to this category.
  • Viral vectors include retrovirus, adenovirus, parvovirus (e.g., adeno-associated viruses), coronavirus, negative strand RNA viruses such as orthomyxovirus (e.g., influenza virus), rhabdovirus (e.g., rabies and vesicular stomatitis virus), paramyxovirus (e.g., measles and Sendai), positive strand RNA viruses such as picornavirus and alphavirus, and double-stranded DNA viruses including adenovirus, herpesvirus (e.g., Herpes Simplex virus types 1 and 2, Epstein-Barr virus, and cytomegalovirus), and poxvirus (e.g., vaccinia, fowlpox, and canarypox).
  • orthomyxovirus e.g., influenza virus
  • rhabdovirus e.g., rabies and vesicular stomatitis virus
  • viruses include, but are not limited to, Norwalk virus, togavirus, flavivirus, reoviruses, papovavirus, hepadnavirus, and hepatitis virus.
  • retroviruses include avian leukosis-sarcoma, mammalian C-type, B-type viruses, D-type viruses, HTLV-BLV group, lentivirus, and spumavirus (Coffin, J. M., Retroviridae: The viruses and their replication, In Fundamental Virology, Third Edition, B. N. Fields, et al., Eds., Lippincott-Raven Publishers, Philadelphia, 1996).
  • “Retroviruses” are viruses having an RNA genome, which is reverse-transcribed into DNA using a reverse transcriptase enzyme, the reverse-transcribed DNA is then incorporated into the host cell genome.
  • “Gammaretrovirus” refers to a genus of the retroviridae family. Examples of gammaretroviruses include mouse stem cell virus, murine leukemia virus, feline leukemia virus, feline sarcoma virus, and avian reticuloendotheliosis viruses.
  • Lentiviral vector refers to HIV-based lentiviral vectors for gene delivery, which can be integrative or non-integrative, have relatively large packaging capacity, and can transduce a range of different cell types. Lentiviral vectors are usually generated following transient transfection of three or more plasmids (packaging, envelope, and transfer) into producer cells. Like HIV, lentiviral vectors enter the target cell through the interaction of viral surface glycoproteins with receptors on the cell surface. On entry, the viral RNA undergoes reverse transcription, which is mediated by the viral reverse transcriptase complex. The product of reverse transcription is a double-stranded linear viral DNA, which is the substrate for viral integration into the DNA of infected cells.
  • lentivirus refers to a genus of retroviruses that are capable of infecting dividing and non-dividing cells.
  • HIV human immunodeficiency virus: including HIV type 1, and HIV type 2
  • equine infectious anemia virus feline immunodeficiency virus (FIV); bovine immune deficiency virus (BIV); and simian immunodeficiency virus (SIV).
  • FIV feline immunodeficiency virus
  • BIV bovine immune deficiency virus
  • SIV simian immunodeficiency virus
  • Other examples include lentivirus vectors derived from HIV-2, FIV, equine infectious anemia virus, SIV, and Maedi-Visna virus (ovine lentivirus).
  • Retroviral and lentiviral viral vectors and packaging cells for transducing mammalian host cells with viral particles containing chimeric antigen receptor transgenes are known in the art and have been previous described, for example, in U.S. Pat. No. 8,119,772; Walchli, et al., PLoS One 6:327930, 2011; Zhao, et al., J. Immunol. 174:4415, 2005; Engels, et al., Hum. Gene Ther. 14: 1155, 2003; Frecha, et al., Mol. Ther. 75: 1748, 2010; and Verhoeyen, et al., Methods Mol. Biol. 506:91, 2009. Retroviral and lentiviral vector constructs and expression systems are also commercially available.
  • the viral vector can be a gammaretrovirus, e.g., Moloney murine leukemia virus (MLV)-derived vectors.
  • the viral vector can be a more complex retrovirus-derived vector, e.g., a lentivirus-derived vector. HIV-1-derived vectors belong to this category.
  • Other examples include lentivirus vectors derived from HIV-2, FIV, equine infectious anemia virus, SIV, and Maedi-Visna virus (ovine lentivirus).
  • Retroviral and lentiviral vector constructs and expression systems are also commercially available.
  • Other viral vectors also can be used for polynucleotide delivery including DNA viral vectors, including, for example adenovirus-based vectors and adeno-associated virus (AAV)-based vectors; vectors derived from herpes simplex viruses (HSVs), including amplicon vectors, replication-defective HSV and attenuated HSV (Krisky et al., Gene Ther. 5:1517, 1998).
  • HSVs herpes simplex viruses
  • vectors developed for gene therapy uses can also be used with the compositions and methods of this disclosure.
  • Such vectors include those derived from baculoviruses and ⁇ -viruses. (Jolly, D J. 1999. Emerging Viral Vectors. pp 209-40 in Friedmann T. ed. The Development of Human Gene Therapy. New York: Cold Spring Harbor Lab), or plasmid vectors (such as Sleeping Beauty or other transposon vectors).
  • the viral vector may also comprise additional sequences between the two (or more) transcripts allowing for bicistronic or multicistronic expression.
  • sequences used in viral vectors include internal ribosome entry sites (IRES), furin cleavage sites, viral 2A peptide, or any combination thereof.
  • the polynucleotide encoding a Msln-specific binding protein may be operatively linked to one or more certain elements of a vector.
  • polynucleotide sequences that are needed to effect the expression and processing of coding sequences to which they are ligated may be operatively linked.
  • Expression control sequences may include appropriate transcription initiation, termination, promoter, and enhancer sequences; efficient RNA processing signals such as splicing and polyadenylation signals; sequences that stabilize cytoplasmic mRNA; sequences that enhance translation efficiency (i.e., Kozak consensus sequences); sequences that enhance protein stability; and possibly sequences that enhance protein secretion.
  • Expression control sequences may be operatively linked if they are contiguous with the gene of interest and expression control sequences that act in trans or at a distance to control the gene of interest.
  • a viral or plasmid vector further includes a transduction marker (e.g., green fluorescent protein, tEGFR, tCD19, tNGFR, etc.).
  • a vector is capable of delivering a polynucleotide construct to a host cell (e.g., a hematopoietic progenitor cell or a human immune system cell).
  • a vector is capable of delivering a construct to human immune system cell, such as, for example, a CD4+ T cell, a CD8+ T cell, a CD4 ⁇ CD8 ⁇ double negative T cell, a ⁇ T cell, a natural killer cell, a dendritic cell, or any combination thereof.
  • a vector is capable of delivering a construct to a na ⁇ ve T cell, a central memory T cell, a stem cell memory T cell, an effector memory T cell, or any combination thereof.
  • a vector that encodes a construct of the present disclosure may further comprise a polynucleotide that encodes a nuclease that can be used to perform a chromosomal knockout in a host cell (e.g., a CRISPR-Cas endonuclease or another endonuclease as disclosed herein) or that can be used to deliver a therapeutic transgene or portion thereof to a host cell in a gene therapy replacement or gene repair therapy.
  • a nuclease used for a chromosomal knockout or a gene replacement or gene repair therapy can be delivered to a host cell independent of a vector that encodes a construct of this disclosure.
  • Construction of an expression vector that is used for recombinantly producing a Msln-specific binding protein can be accomplished by using any suitable molecular biology engineering techniques known in the art, including the use of restriction endonuclease digestion, ligation, transformation, plasmid purification, and DNA sequencing, for example as described in Sambrook, et al. (1989 and 2001 editions; Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, NY) and Ausubel, et al. (Current Protocols in Molecular Biology (2003)).
  • a polynucleotide in each recombinant expression construct includes at least one appropriate expression control sequence (also called a regulatory sequence), such as a leader sequence and particularly a promoter operably (i.e., operatively) linked to the nucleotide sequence encoding the protein or peptide of interest.
  • a regulatory sequence also called a regulatory sequence
  • a promoter operably (i.e., operatively) linked to the nucleotide sequence encoding the protein or peptide of interest.
  • nucleic acid molecules encoding a binding protein specific for a Msln 20-28 or Msln 530-538 peptide are used to transfect/transduce a host cell (e.g., T cells) for use in adoptive transfer therapy.
  • a host cell e.g., T cells
  • Advances in TCR sequencing have been described (e.g., Robins, et al, 2009 Blood 114:4099; Robins, et al, 2010 Sci. Translat. Med. 2:47ra64, PMID: 20811043; Robins, et al. 2011 (Sep. 10) J. 1 mm. Meth. Epub ahead of print, PMID: 21945395; and Warren, et al., 2011 Genome Res. 21:790) and may be employed in the course of practicing the embodiments according to the present disclosure.
  • the recombinant expression vectors may include, for example, lymphoid tissue-specific transcriptional regulatory elements (TRE) such as a B lymphocyte, T lymphocyte, or dendritic cell specific TRE.
  • TRE lymphoid tissue-specific transcriptional regulatory elements
  • Lymphoid tissue specific TRE are known in the art (see, e.g., Thompson, et al., Mol. Cell. Biol. 72:1043, (1992); Todd et al, J. Exp. Med. 177: 1663, (1993); and Penix, et al., J. Exp. Med. 775: 1483, (1993)).
  • recombinant (e.g., modified) host cells that encode (e.g., comprise a heterologous polynucleotide encoding) and/or express a Msln-specific binding protein as disclosed herein.
  • the host cell may be a hematopoietic progenitor cell or an immune system cell as disclosed herein, such as a human immune system cell.
  • the immune system cell is a CD4+ T cell, a CD8+ T cell, a CD4 ⁇ CD8 ⁇ double negative T cell, a ⁇ T cell, a natural killer cell, a natural kill T cell, a macrophage, a dendritic cell, or any combination thereof.
  • the T cell may be a na ⁇ ve T cell, a central memory T cell, an effector memory T cell, a stem cell memory T cell, or any combination thereof.
  • the host cell is modified to comprise or contain the heterologous polynucleotide using a vector as disclosed herein.
  • the recombinant host cell may be allogeneic, syngeneic, or autologous (e.g., to a subject that receives the host cell for a therapy).
  • the heterologous binding protein or TCR expressed by the T cell is capable of more efficiently associating with a CD3 protein as compared to an endogenous TCR.
  • the Msln-specific binding protein expressed by a host T cell is able to associate with the CD3 complex and shows functional surface expression and immune activity, e.g., production of cytokines and/or killing of antigen-expressing target cells.
  • the Msln-specific binding protein may have higher cell surface expression as compared to an endogenous TCR.
  • a host cell such as a host immune cell
  • a host immune cell can comprise a chromosomal gene knockout of an endogenous immune cell protein, such as, for example, PD-1, TIM3, LAG3, CTLA4, TIGIT, an HLA component, or a TCR component, or any combination thereof.
  • an endogenous immune cell protein such as, for example, PD-1, TIM3, LAG3, CTLA4, TIGIT, an HLA component, or a TCR component, or any combination thereof.
  • the term “chromosomal gene knockout” refers to a genetic alteration or introduced inhibitory agent in a host cell that prevents (e.g., reduces, delays, suppresses, or abrogates) production, by the host cell, of a functionally active endogenous polypeptide product.
  • Alterations resulting in a chromosomal gene knockout can include, for example, introduced nonsense mutations (including the formation of premature stop codons), missense mutations, gene deletion, and strand breaks, as well as the heterologous expression of inhibitory nucleic acid molecules that inhibit endogenous gene expression in the host cell.
  • Chromosomal gene knockout can be confirmed directly by DNA sequencing of the host immune cell following use of the knockout procedure or agent. Chromosomal gene knockouts can also be inferred from the absence of gene expression (e.g., the absence of an mRNA or polypeptide product encoded by the gene) following the knockout.
  • a chromosomal gene knock-out or gene knock-in is made by chromosomal editing of a host cell.
  • Chromosomal editing can be performed using, for example, endonucleases.
  • endonucleases refers to an enzyme capable of catalyzing cleavage of a phosphodiester bond within a polynucleotide chain.
  • an endonuclease is capable of cleaving a targeted gene thereby inactivating or “knocking out” the targeted gene.
  • An endonuclease may be a naturally occurring, recombinant, genetically modified, or fusion endonuclease.
  • the nucleic acid strand breaks caused by the endonuclease are commonly repaired through the distinct mechanisms of homologous recombination or non-homologous end joining (NHEJ).
  • NHEJ non-homologous end joining
  • a donor nucleic acid molecule may be used for a donor gene “knock-in”, for target gene “knock-out”, and optionally to inactivate a target gene through a donor gene knock in or target gene knock out event.
  • NHEJ is an error-prone repair process that often results in changes to the DNA sequence at the site of the cleavage, e.g., a substitution, deletion, or addition of at least one nucleotide.
  • NHEJ may be used to “knock-out” a target gene.
  • Examples of endonucleases include zinc finger nucleases, TALE-nucleases, CRISPR-Cas nucleases, meganucleases, and megaTALs.
  • a “zinc finger nuclease” refers to a fusion protein comprising a zinc finger DNA-binding domain fused to a non-specific DNA cleavage domain, such as a Fokl endonuclease.
  • ZFN zinc finger nuclease
  • Each zinc finger motif of about 30 amino acids binds to about 3 base pairs of DNA, and amino acids at certain residues can be changed to alter triplet sequence specificity (see, e.g., Desjarlais et al., Proc. Natl. Acad. Sci. 90:2256-2260, 1993; Wolfe et al., J. Mol. Biol. 285:1917-1934, 1999).
  • ZFNs mediate genome editing by catalyzing the formation of a site-specific DNA double strand break (DSB) in the genome, and targeted integration of a transgene comprising flanking sequences homologous to the genome at the site of DSB is facilitated by homology directed repair.
  • DSB DNA double strand break
  • a DSB generated by a ZFN can result in knock out of target gene via repair by non-homologous end joining (NHEJ), which is an error-prone cellular repair pathway that results in the insertion or deletion of nucleotides at the cleavage site.
  • NHEJ non-homologous end joining
  • a gene knockout comprises an insertion, a deletion, a mutation or a combination thereof, made using a ZFN molecule.
  • TALEN transcription activator-like effector nuclease
  • a “TALE DNA binding domain” or “TALE” is composed of one or more TALE repeat domains/units, each generally having a highly conserved 33-35 amino acid sequence with divergent 12th and 13th amino acids.
  • the TALE repeat domains are involved in binding of the TALE to a target DNA sequence.
  • the divergent amino acid residues referred to as the Repeat Variable Diresidue (RVD), correlate with specific nucleotide recognition.
  • RVD Repeat Variable Diresidue
  • the natural (canonical) code for DNA recognition of these TALEs has been determined such that an HD (histine-aspartic acid) sequence at positions 12 and 13 of the TALE leads to the TALE binding to cytosine (C), NG (asparagine-glycine) binds to a T nucleotide, NI (asparagine-isoleucine) to A, NN (asparagine-asparagine) binds to a G or A nucleotide, and NG (asparagine-glycine) binds to a T nucleotide.
  • Non-canonical (atypical) RVDs are also known (see, e.g., U.S. Patent Publication No.
  • TALENs can be used to direct site-specific double-strand breaks (DSB) in the genome of T cells.
  • Non-homologous end joining (NHEJ) ligates DNA from both sides of a double-strand break in which there is little or no sequence overlap for annealing, thereby introducing errors that knock out gene expression.
  • homology directed repair can introduce a transgene at the site of DSB providing homologous flanking sequences are present in the transgene.
  • a gene knockout comprises an insertion, a deletion, a mutation or a combination thereof, and made using a TALEN molecule.
  • CRISPR/Cas nuclease system refers to a system that employs a CRISPR RNA (crRNA)-guided Cas nuclease to recognize target sites within a genome (known as protospacers) via base-pairing complementarity and then to cleave the DNA if a short, conserved protospacer associated motif (PAM) immediately follows 3′ of the complementary target sequence.
  • CRISPR/Cas systems are classified into three types (i.e., type I, type II, and type III) based on the sequence and structure of the Cas nucleases.
  • the crRNA-guided surveillance complexes in types I and III need multiple Cas subunits.
  • Type II system the most studied, comprises at least three components: an RNA-guided Cas9 nuclease, a crRNA, and a trans-acting crRNA (tracrRNA).
  • the tracrRNA comprises a duplex forming region.
  • a crRNA and a tracrRNA form a duplex that is capable of interacting with a Cas9 nuclease and guiding the Cas9/crRNA:tracrRNA complex to a specific site on the target DNA via Watson-Crick base-pairing between the spacer on the crRNA and the protospacer on the target DNA upstream from a PAM.
  • Cas9 nuclease cleaves a double-stranded break within a region defined by the crRNA spacer. Repair by NHEJ results in insertions and/or deletions which disrupt expression of the targeted locus.
  • a transgene with homologous flanking sequences can be introduced at the site of DSB via homology directed repair.
  • the crRNA and tracrRNA can be engineered into a single guide RNA (sgRNA or gRNA) (see, e.g., Jinek et al., Science 337:816-21, 2012).
  • a gene knockout comprises an insertion, a deletion, a mutation or a combination thereof, and made using a CRISPR/Cas nuclease system.
  • Exemplary gRNA sequences and methods of using the same to knock out endogenous genes that encode immune cell proteins include those described in Ren et al., Clin. Cancer Res. 23(9):2255-2266 (2017), the gRNAs, CAS9 DNAs, vectors, and gene knockout techniques of which are hereby incorporated by reference in their entirety.
  • Exemplary meganucleases include I-SceI, I-CeuI, PI-PspI, PI-Sce, I-SceIV, I-CsmI, I-PanI, I-SceII, I-PpoI, I-SceIII, I-CreI, I-TevI, I-TevII and I-TevIII, whose recognition sequences are known (see, e.g., U.S. Pat. Nos. 5,420,032 and 6,833,252; Belfort et al., Nucleic Acids Res.
  • naturally-occurring meganucleases may be used to promote site-specific genome modification of a target selected from PD-1, LAG3, TIM3, CTLA4, TIGIT, an HLA-encoding gene, or a TCR component-encoding gene.
  • an engineered meganuclease having a novel binding specificity for a target gene is used for site-specific genome modification (see, e.g., Porteus et al., Nat. Biotechnol. 23:967-73, 2005; Sussman et al., J. Mol. Biol. 342:31-41, 2004; Epinat et al., Nucleic Acids Res. 31:2952-62, 2003; Chevalier et al., Molec. Cell 10:895-905, 2002; Ashworth et al., Nature 441:656-659, 2006; Paques et al., Curr. Gene Ther. 7:49-66, 2007; U.S.
  • a chromosomal gene knockout is generated using a homing endonuclease that has been modified with modular DNA binding domains of TALENs to make a fusion protein known as a megaTAL.
  • MegaTALs can be utilized to not only knock-out one or more target genes, but to also introduce (knock in) heterologous or exogenous polynucleotides when used in combination with an exogenous donor template encoding a polypeptide of interest.
  • a chromosomal gene knockout comprises an inhibitory nucleic acid molecule that is introduced into a host cell (e.g., an immune cell) comprising a heterologous polynucleotide encoding an antigen-specific receptor that specifically binds to a tumor associated antigen, wherein the inhibitory nucleic acid molecule encodes a target-specific inhibitor and wherein the encoded target-specific inhibitor inhibits endogenous gene expression (i.e., of PD-1, TIM3, LAG3, CTLA4, TIGIT, an HLA component, or a TCR component, or any combination thereof) in the host immune cell.
  • a host cell e.g., an immune cell
  • a heterologous polynucleotide encoding an antigen-specific receptor that specifically binds to a tumor associated antigen
  • the inhibitory nucleic acid molecule encodes a target-specific inhibitor and wherein the encoded target-specific inhibitor inhibits endogenous gene expression (i.e., of PD-1,
  • a binding protein of interest may be knocked-in to a host cell; e.g., using any of the presently disclosed techniques or reagents useful for knocking a polynucleotide of interest into a host cell.
  • a polynucleotide encoding a binding protein is knocked-in to a host cell and does not integrate into an endogenous chromosome, such as in the cell nucleus.
  • a polynucleotide encoding a binding protein is knocked-in to a host cell at an endogenous gene locus, optionally disrupting a coding sequence of the endogenous locus.
  • a polynucleotide encoding a binding protein is knocked-in to an endogenous TCR locus, thereby knocking-out endogenous TCR and knocking-in the protein of interest. See, e.g., Eyquem et al., Nature 543(7643):113-117 (2017).
  • a polynucleotide encoding a mesothelin-specific binding protein (e.g., a polypeptide comprising, consisting, or consisting essentially of the amino acid sequence set forth in any one or more of SEQ ID Nos:6-8, 14-16, 22-24, 28-40, 78-110, 118, 119) is knocked-in to a host cell.
  • Binding proteins herein include a TCR alpha chain variable domain (V ⁇ ) and a TCR beta chain variable domain (V ⁇ ).
  • a mesothelin-specific binding protein is capable of specifically binding to a mesothelin peptide:HLA complex, such as a mesothelin peptide:HLA-A*02:01 complex.
  • gene knock-in may be used to introduce a polynucleotide encoding a binding protein that is capable of specifically binding to a mesothelin peptide antigen as described herein (e.g., a peptide comprising, consisting, or consisting essentially of an amino acid sequence having at least about 85% (i.e., at least about 86%, 85%, 88%, 89% 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more) identity to the amino acid sequence set forth in any one or more of SEQ ID Nos:6-8, 14-16, 22-24, 28-40, 78-110, 118, or 119).
  • a polynucleotide encoding a mesothelin-specific binding protein is knocked-in to a host cell, and the host cell further comprises a polynucleotide encoding a different binding protein.
  • the different binding protein is heterologous to the host cell.
  • the different binding protein is endogenous to the host cell.
  • the polynucleotide encoding the different binding protein is knocked-in to the host cell.
  • the different binding protein is a binding protein specific for a different antigen (e.g., a different Msln antigen, or an antigen from a different protein or target, such as, for example, BCMA, CA19-9, BRAF, CD3, CEACAM6, c-Met, EGFR, EGFRvIII, ErbB2, ErbB3, ErbB4, EphA2, IGF1R, GD2, O-acetyl GD2, O-acetyl GD3, GHRHR, GHR, FLT1, KDR, FLT4, CD44v6, CD151, CA125, CEA, CTLA-4, GITR, BTLA, TGFBR2, TGFBR1, IL6R, gp130, Lewis A, Lewis Y, TNFR1, TNFR2, PD1, PD-L1, PD-L2, HVEM, MAGE-A (e.g., including MAGE-A1, MAGE-A3, and MAGE-A4), KRAS, HER2, NY
  • a host cell can comprise a knocked-in polynucleotide encoding a binding protein that specifically binds to a Msln antigen:HLA complex and a (e.g., knocked-in) polynucleotide encoding a binding protein (e.g., a TCR or a CAR) that specifically binds to a CA19-9 antigen.
  • a knocked-in polynucleotide encoding a binding protein that specifically binds to a Msln antigen:HLA complex
  • a (e.g., knocked-in) polynucleotide encoding a binding protein (e.g., a TCR or a CAR) that specifically binds to a CA19-9 antigen.
  • a host immune cell encoding and/or expressing a Msln-specific binding protein of the present disclosure is capable of preferentially migrating to or localizing in vivo in a target tissue that expresses a cognate Msln antigen, such as a tumor, but is present at a statistically significant reduced amount in non-adjacent tissue of the same type.
  • a host immune cell may be present in a lung tumor (e.g., as determined using deep sequencing for the TCR V-region of the encoded binding protein), but is present at a lower level, or not at all, in tissue of the same lung that is not adjacent to the tumor.
  • non-adjacent tissue comprises or refers to tissue that is removed from a diseased or malignant tissue by at least 3 cm.
  • a host cell is enriched in a composition of cells, such as may be administered to a subject.
  • enriched or “depleted” with respect to amounts of cell types in a mixture refers to an increase in the number of the “enriched” type, a decrease in the number of the “depleted” cells, or both, in a mixture of cells resulting from one or more enriching or depleting processes or steps.
  • a mixture or composition may contain 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more (in number or count) of the “enriched” cells.
  • Cells subjected to a depleting process can result in a mixture or composition containing 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or 1% percent or less (in number or count) of the “depleted” cells.
  • amounts of a certain cell type in a mixture will be enriched and amounts of a different cell type will be depleted, such as enriching for CD4+ cells while depleting CD8+ cells, or enriching for CD62L+ cells while depleting CD62L ⁇ cells, or combinations thereof.
  • the present disclosure provides methods treating a subject in need thereof (i.e., having or suspected of having a disease or disorder associated with a mesothelin antigen by administering to the subject an effective amount of a composition (e.g., binding protein, recombinant host cell, polynucleotide, vector, or related composition) as described herein.
  • a composition e.g., binding protein, recombinant host cell, polynucleotide, vector, or related composition
  • Such compositions for use in treating such a disease, or for the manufacture of a medicament for the treatment of such a disease.
  • diseases include various forms of proliferative or hyperproliferative disorders, such as solid cancers and hematological malignancies.
  • Treatment refers to medical management of a disease, disorder, or condition of a subject (e.g., a human or non-human mammal, such as a primate, horse, cat, dog, goat, mouse, or rat).
  • a subject e.g., a human or non-human mammal, such as a primate, horse, cat, dog, goat, mouse, or rat.
  • an appropriate dose or treatment regimen comprising a host cell expressing a binding protein of the present disclosure, and optionally an adjuvant, is administered in an amount sufficient to elicit a therapeutic or prophylactic benefit.
  • Therapeutic or prophylactic/preventive benefit includes improved clinical outcome; lessening or alleviation of symptoms associated with a disease; decreased occurrence of symptoms; improved quality of life; longer disease-free status; diminishment of extent of disease; stabilization of disease state; delay of disease progression; remission; survival; prolonged survival; or any combination thereof.
  • adoptive immune therapy or “adoptive immunotherapy” and “adoptive cell therapy” refer to administration of naturally occurring or genetically engineered, disease-antigen-specific immune cells (e.g., T cells).
  • adoptive cellular immunotherapy may be autologous (immune cells are from the recipient), allogeneic (immune cells are from a donor of the same species) or syngeneic (immune cells are from a donor genetically identical to the recipient).
  • a “therapeutically effective amount” or “effective amount” of a binding protein or host cell of this disclosure refers to an amount of binding proteins or host cells sufficient to result in a therapeutic effect, including improved clinical outcome; lessening or alleviation of symptoms associated with a disease; decreased occurrence of symptoms; improved quality of life; longer disease-free status; diminishment of extent of disease, stabilization of disease state; delay of disease progression; remission; survival; or prolonged survival in a statistically significant manner.
  • a therapeutically effective amount refers to the effects of that ingredient or cell expressing that ingredient alone.
  • a therapeutically effective amount refers to the combined amounts of active ingredients or combined adjunctive active ingredient with a cell expressing an active ingredient that results in a therapeutic effect, whether administered serially or simultaneously.
  • a combination may also be a cell expressing more than one active ingredient, such as two different binding proteins that specifically bind an antigen, or a fusion protein of the present disclosure.
  • statically significant refers to a p-value of 0.050 or less when calculated using the Student's t-test and indicates that it is unlikely that a particular event or result being measured has arisen by chance.
  • hyperproliferative disorder refers to excessive growth or proliferation as compared to a normal or undiseased cell.
  • exemplary hyperproliferative disorders include tumors, cancers, neoplastic tissue, carcinoma, sarcoma, malignant cells, pre malignant cells, as well as non-neoplastic or non-malignant hyperproliferative disorders (e.g., adenoma, fibroma, lipoma, leiomyoma, hemangioma, fibrosis, restenosis, as well as autoimmune diseases such as rheumatoid arthritis, osteoarthritis, psoriasis, inflammatory bowel disease, or the like).
  • Certain diseases that involve abnormal or excessive growth that occurs more slowly than in the context of a hyperproliferative disease can be referred to as “proliferative diseases”, and include certain tumors, cancers, neoplastic tissue, carcinoma, sarcoma, malignant cells, pre malignant cells, as well as non-neoplastic or non-malignant disorders.
  • cancer may refer to any accelerated proliferation of cells, including solid tumors, ascites tumors, blood or lymph or other malignancies; connective tissue malignancies; metastatic disease; minimal residual disease following transplantation of organs or stem cells; multi-drug resistant cancers, primary or secondary malignancies, angiogenesis related to malignancy, or other forms of cancer.
  • binding proteins, host cells, polynucleotides, vectors, and compositions are useful to treat or manufacture a medicament for the treatment a cancer wherein a Msln 20-28 peptide is expressed on a tumor cell of the cancer, and/or wherein a Msln 530-538 peptide is expressed on a tumor cell of the cancer;
  • exemplary cancers for treatment include mesothelioma, pancreatic cancer, ovarian cancer, and lung cancer.
  • the presently disclosed binding proteins, host cells, polynucleotides, vectors, and compositions are useful for treating and/or in the manufacture of a medicament for treating a cancer, such as a solid cancer or a hematological malignancy.
  • the solid cancer is selected from or comprises biliary cancer, bladder cancer, bone and soft tissue carcinoma, brain tumor, breast cancer, cervical cancer, colon cancer, colorectal adenocarcinoma, colorectal cancer, desmoid tumor, embryonal cancer, endometrial cancer, esophageal cancer, gastric cancer, gastric adenocarcinoma, glioblastoma multiforme, gynecological tumor, head and neck squamous cell carcinoma, hepatic cancer, lung cancer, mesothelioma, malignant melanoma, osteosarcoma, ovarian cancer, pancreatic cancer, pancreatic ductal adenocarcinoma, primary astrocytic tumor, primary thyroid cancer, prostate cancer, renal cancer, renal cell carcinoma, rhabdomyosarcoma, skin cancer, soft tissue sarcoma, testicular germ-cell tumor, urothelial cancer, uterine sarcoma, or
  • a cancer treatable according to the presently disclosed methods and uses comprises a carcinoma, a sarcoma, a glioma, a lymphoma, a leukemia, a myeloma, or any combination thereof.
  • cancer comprises a cancer of the head or neck, melanoma, pancreatic cancer, cholangiocarcinoma, hepatocellular cancer, breast cancer including triple-negative breast cancer (TNBC), gastric cancer, non-small-cell lung cancer, prostate cancer, esophageal cancer, mesothelioma, small-cell lung cancer, colorectal cancer, glioblastoma, or any combination thereof.
  • TNBC triple-negative breast cancer
  • a cancer comprises Askin's tumor, sarcoma botryoides, chondrosarcoma, Ewing's sarcoma, PNET, malignant hemangioendothelioma, malignant schwannoma, osteosarcoma, alveolar soft part sarcoma, angiosarcoma, cystosarcoma phyllodes, dermatofibrosarcoma protuberans (DFSP), desmoid tumor, desmoplastic small round cell tumor, epithelioid sarcoma, extraskeletal chondrosarcoma, extraskeletal osteosarcoma, fibrosarcoma, gastrointestinal stromal tumor (GIST), hemangiopericytoma, hemangiosarcoma, Kaposi's sarcoma, leiomyosarcoma, liposarcoma, lymphangiosarcoma, lymphosarcoma, undifferentiated pleomorphic sarcoma,
  • the cancer comprises a solid tumor.
  • the solid tumor is a sarcoma or a carcinoma.
  • the solid tumor is selected from: chondrosarcoma; fibrosarcoma (fibroblastic sarcoma); Dermatofibrosarcoma protuberans (DF SP); osteosarcoma; rhabdomyosarcoma; Ewing's sarcoma; a gastrointestinal stromal tumor; Leiomyosarcoma; angiosarcoma (vascular sarcoma); Kaposi's sarcoma; liposarcoma; pleomorphic sarcoma; or synovial sarcoma.
  • the solid tumor is selected from a lung carcinoma (e.g., Adenocarcinoma, Squamous Cell Carcinoma (Epidermoid Carcinoma); Squamous cell carcinoma; Adenocarcinoma; Adenosquamous carcinoma; anaplastic carcinoma; Large cell carcinoma; Small cell carcinoma; a breast carcinoma (e.g., Ductal Carcinoma in situ (non-invasive), Lobular carcinoma in situ (non-invasive), Invasive Ductal Carcinoma, Invasive lobular carcinoma, Non-invasive Carcinoma); a liver carcinoma (e.g., Hepatocellular Carcinoma, Cholangiocarcinomas or Bile Duct Cancer); Large-cell undifferentiated carcinoma, Bronchioalveolar carcinoma); an ovarian carcinoma (e.g., Surface epithelial-stromal tumor (Adenocarcinoma) or ovarian epithelial carcinoma (which includes serous tumor, endometrioid tumor and m
  • the solid tumor is an ovarian carcinoma, an ovarian epithelial carcinoma, a cervical adenocarcinoma or small cell carcinoma, a pancreatic carcinoma, a colorectal carcinoma (e.g., an adenocarcinoma or squamous cell carcinoma), a lung carcinoma, a breast ductal carcinoma, or an adenocarcinoma of the prostate.
  • the host cell is an allogeneic cell, a syngeneic cell, or an autologous cell.
  • Subjects that can be treated by the present invention are, in general, human and other primate subjects, such as monkeys and apes for veterinary medicine purposes.
  • the subject may be a human subject.
  • the subjects can be male or female and can be any suitable age, including infant, juvenile, adolescent, adult, and geriatric subjects.
  • Cells according to the present disclosure may be administered in a manner appropriate to the disease, condition, or disorder to be treated as determined by persons skilled in the medical art.
  • a cell comprising a fusion protein as described herein is administered intravenously, intraperitoneally, intratumorally, into the bone marrow, into a lymph node, or into the cerebrospinal fluid so as to encounter the tagged cells to be ablated.
  • An appropriate dose, suitable duration, and frequency of administration of the compositions will be determined by such factors as a condition of the patient; size, type, and severity of the disease, condition, or disorder; the undesired type or level or activity of the tagged cells, the particular form of the active ingredient; and the method of administration.
  • an appropriate dosage and treatment regimen provides the active molecules or cells in an amount sufficient to provide a benefit.
  • a response can be monitored by establishing an improved clinical outcome (e.g., more frequent remissions, complete or partial, or longer disease-free survival) in treated subjects as compared to non-treated subjects.
  • Increases in preexisting immune responses to a tumor protein generally correlate with an improved clinical outcome.
  • Such immune responses may generally be evaluated using standard proliferation, cytotoxicity or cytokine assays, which are routine.
  • a dose should be sufficient to prevent, delay the onset of, or diminish the severity of a disease associated with disease or disorder.
  • Prophylactic benefit of the immunogenic compositions administered according to the methods described herein can be determined by performing pre-clinical (including in vitro and in vivo animal studies) and clinical studies and analyzing data obtained therefrom by appropriate statistical, biological, and clinical methods and techniques, all of which can readily be practiced by a person skilled in the art.
  • an effective dose is an amount of host cells encoding or expressing a Msln-specific binding protein used in adoptive transfer that is capable of producing a clinically desirable result (i.e., a sufficient amount to induce or enhance a specific T cell immune response against cells expressing an Msln-specific antigen response, e.g., a cytotoxic T cell response, in a statistically significant manner) in a treated human or non-human mammal.
  • T cell is a na ⁇ ve T cell, a central memory T cell, a stem cell memory T cell, an effector memory T cell, or any combination thereof.
  • compositions that comprise a Msln-specific binding protein, host (i.e., modified) immune cell, polynucleotide, or vector as disclosed herein and a pharmaceutically acceptable carrier, diluents, or excipient.
  • pharmaceutically acceptable excipient or carrier or “physiologically acceptable excipient or carrier” refer to biologically compatible vehicles, e.g., physiological saline, which are described in greater detail herein, that are suitable for administration to a human or other non-human mammalian subject and generally recognized as safe or not causing a serious adverse event.
  • Suitable excipients include water, saline, dextrose, glycerol, or the like and combinations thereof.
  • compositions comprising fusion proteins or host cells as disclosed herein further comprise a suitable infusion media.
  • suitable infusion media can be any isotonic medium formulation, typically normal saline, Normosol R (Abbott) or Plasma-Lyte A (Baxter), 5% dextrose in water, Ringer's lactate can be utilized.
  • An infusion medium can be supplemented with human serum albumin or other human serum components.
  • compositions may be administered in a manner appropriate to the disease or condition to be treated (or prevented) as determined by persons skilled in the medical art.
  • An appropriate dose and a suitable duration and frequency of administration of the compositions will be determined by such factors as the health condition of the patient, size of the patient (i.e., weight, mass, or body area), the type and severity of the patient's condition, the particular form of the active ingredient, and the method of administration.
  • an appropriate dose and treatment regimen provide the composition(s) in an amount sufficient to provide therapeutic and/or prophylactic benefit (such as described herein, including an improved clinical outcome, such as more frequent complete or partial remissions, or longer disease-free and/or overall survival, or a lessening of symptom severity).
  • a unit dose comprises (i) a composition comprising at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% modified CD4+ T cells, combined with (ii) a composition comprising at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% modified CD8+ T cells, in about a 1:1 ratio, wherein the unit dose contains a reduced amount or substantially no na ⁇ ve T cells (i.e., has less than about 50%, less than about 40%, less than about 30%, less than about 20%, less than about 10%, less than about 5%, or less then about 1% the population of na ⁇ ve T cells present in a
  • a unit dose comprises (i) a composition comprising at least about 50% modified CD4+ T cells, combined with (ii) a composition comprising at least about 50% modified CD8+ T cells, in about a 1:1 ratio, wherein the unit dose contains a reduced amount or substantially no na ⁇ ve T cells.
  • a unit dose comprises (i) a composition comprising at least about 60% modified CD4+ T cells, combined with (ii) a composition comprising at least about 60% modified CD8+ T cells, in about a 1:1 ratio, wherein the unit dose contains a reduced amount or substantially no na ⁇ ve T cells.
  • a unit dose comprises (i) a composition comprising at least about 70% engineered CD4+ T cells, combined with (ii) a composition comprising at least about 70% engineered CD8+ T cells, in about a 1:1 ratio, wherein the unit dose contains a reduced amount or substantially no na ⁇ ve T cells.
  • a unit dose comprises (i) a composition comprising at least about 80% modified CD4+ T cells, combined with (ii) a composition comprising at least about 80% modified CD8+ T cells, in about a 1:1 ratio, wherein the unit dose contains a reduced amount or substantially no na ⁇ ve T cells.
  • a unit dose comprises (i) a composition comprising at least about 85% modified CD4+ T cells, combined with (ii) a composition comprising at least about 85% modified CD8+ T cells, in about a 1:1 ratio, wherein the unit dose contains a reduced amount or substantially no na ⁇ ve T cells.
  • a unit dose comprises (i) a composition comprising at least about 90% modified CD4+ T cells, combined with (ii) a composition comprising at least about 90% modified CD8+ T cells, in about a 1:1 ratio, wherein the unit dose contains a reduced amount or substantially no na ⁇ ve T cells.
  • the amount of cells in a composition or unit dose is at least one cell (for example, one recombinant CD8+ T cell subpopulation (e.g., optionally comprising memory and/or na ⁇ ve CD8+ T cells); one recombinant CD4+ T cell subpopulation (e.g., optionally comprising memory and/or na ⁇ ve CD4+ T cells)) or is more typically greater than 10 2 cells, for example, up to 10 4 , up to 10 5 , up to 10 6 , up to 10 7 , up to 10 8 , up to 10 9 , or more than 10 10 cells.
  • the cells are administered in a range from about 10 4 to about 10 10 cells/m 2 , preferably in a range of about 10 5 to about 10 9 cells/m 2 .
  • an administered dose comprises up to about 3.3 ⁇ 10 5 cells/kg.
  • an administered dose comprises up to about 1 ⁇ 10 6 cells/kg.
  • an administered dose comprises up to about 3.3 ⁇ 10 6 cells/kg.
  • an administered dose comprises up to about 1 ⁇ 10 7 cells/kg.
  • a recombinant host cell is administered to a subject at a dose comprising up to about 5 ⁇ 10 4 cells/kg, 5 ⁇ 10 5 cells/kg, 5 ⁇ 10 6 cells/kg, or up to about 5 ⁇ 10 7 cells/kg. In certain embodiments, a recombinant host cell is administered to a subject at a dose comprising at least about 5 ⁇ 10 4 cells/kg, 5 ⁇ 10 5 cells/kg, 5 ⁇ 10 6 cells/kg, or up to about 5 ⁇ 10 7 cells/kg. The number of cells will depend upon the ultimate use for which the composition is intended as well the type of cells included therein.
  • cells modified to express or encode a binding protein will comprise a cell population containing at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or more of such cells.
  • cells are generally in a volume of a liter or less, 500 mls or less, 250 mls or less, or 100 mls or less.
  • the density of the desired cells is typically greater than 10 4 cells/ml and generally is greater than 10 7 cells/ml, generally 10 8 cells/ml or greater.
  • the cells may be administered as a single infusion or in multiple infusions over a range of time.
  • a clinically relevant number of cells can be apportioned into multiple infusions that cumulatively equal or exceed 10 6 , 10 7 , 10 8 , 10 9 , 10 10 , or 10 11 cells.
  • a unit dose of the cells can be co-administered with (e.g., simultaneously or contemporaneously with) hematopoietic stem cells from an allogeneic donor.
  • one or more of the cells comprised in the unit dose is autologous to the subject.
  • a unit dose, composition, or treatment regimen of the present disclosure may comprise a Msln-specific binding protein or recombinant host cell as described herein, and also comprise an (e.g., modified) immune cell expressing a binding protein specific for a different antigen (e.g., a different Msln antigen, or an antigen from a different protein or target, such as, for example, BCMA, CA19-9, BRAF, CD3, CEACAM6, c-Met, EGFR, EGFRvIII, ErbB2, ErbB3, ErbB4, EphA2, IGF1R, GD2, O-acetyl GD2, O-acetyl GD3, GHRHR, GHR, FLT1, KDR, FLT4, CD44v6, CD151, CA125, CEA, CTLA-4, GITR, BTLA, TGFBR2, TGFBR1, IL6R, gp130, Lewis A, Lewis Y, TNFR1, TNFR2, PD1,
  • a unit dose or therapeutic regimen can comprise modified CD4+ T cells expressing a binding protein that specifically binds to a Msln antigen:HLA complex and modified CD4+ T cells (and/or modified CD8+ T cells) expressing a binding protein (e.g., a TCR or a CAR) that specifically binds to a CA19-9 antigen.
  • a binding protein e.g., a TCR or a CAR
  • a unit dose comprises equal, or approximately equal, numbers of engineered CD45RA ⁇ CD3+CD8+ and modified CD45RA ⁇ CD3+CD4+ TM cells.
  • compositions described herein may be presented in unit-dose or multi-dose containers, such as sealed ampoules or vials. Such containers may be frozen to preserve the stability of the formulation until infusion into the patient.
  • administration of a composition refers to delivering the same to a subject, regardless of the route or mode of delivery, such as, for example, intravenous, oral vaginal, rectal, subcutaneous, or the like. Administration may be effected continuously or intermittently, and parenterally. Administration may be for treating a subject already confirmed as having a recognized condition, disease or disease state, or for treating a subject susceptible to or at risk of developing such a condition, disease or disease state.
  • Co-administration with an adjunctive therapy may include simultaneous and/or sequential delivery of multiple agents in any order and on any dosing schedule (e.g., recombinant host cells with one or more cytokines; immunosuppressive therapy such as calcineurin inhibitors, corticosteroids, microtubule inhibitors, low dose of a mycophenolic acid prodrug, or any combination thereof).
  • a dosing schedule e.g., recombinant host cells with one or more cytokines; immunosuppressive therapy such as calcineurin inhibitors, corticosteroids, microtubule inhibitors, low dose of a mycophenolic acid prodrug, or any combination thereof.
  • the composition may also include sterile aqueous or oleaginous solution or suspension.
  • suitable non-toxic parenterally acceptable diluents or solvents include water, Ringer's solution, isotonic salt solution, 1,3-butanediol, ethanol, propylene glycol, or polyethylene glycols in mixtures with water.
  • Aqueous solutions or suspensions may further include one or more buffering agents, such as sodium acetate, sodium citrate, sodium borate, or sodium tartrate.
  • any material used in preparing any dosage unit formulation should be pharmaceutically pure and substantially non-toxic in the amounts employed.
  • the active compounds may be incorporated into sustained-release preparation and formulations.
  • Dosage unit form refers to physically discrete units suited as unitary dosages for the subject to be treated; each unit may contain a predetermined quantity of recombinant cells or active compound calculated to produce the desired therapeutic effect in association with an appropriate pharmaceutical carrier.
  • a plurality of doses of a composition described herein is administered to the subject, which may be administered at intervals between administrations of about two to about four weeks.
  • Treatment or prevention methods of this disclosure may be administered to a subject as part of a treatment course or regimen, which may comprise additional treatments prior to, or after, administration of the instantly disclosed unit doses, cells, or compositions.
  • a subject receiving a unit dose of the e.g., a recombinant host cell is receiving or had previously received a hematopoietic cell transplant (HCT; including myeloablative and non-myeloablative HCT).
  • HCT hematopoietic cell transplant
  • a recombinant host cell of the present disclosure can be administered with or shortly after hematopoietic stem cells in a modified HCT therapy.
  • the HCT comprises a donor hematopoietic cell comprising a chromosomal knockout of a gene that encodes an HLA component, a chromosomal knockout of a gene that encodes a TCR component, or both.
  • the level of a CTL immune response may be determined by any one of numerous immunological methods described herein and routinely practiced in the art.
  • the level of a CTL immune response may be determined prior to and following administration of any one of the herein described Msln-specific binding proteins (or a host cell encoding and/or expressing the same) or immunogenic compositions.
  • Cytotoxicity assays for determining CTL activity may be performed using any one of several techniques and methods routinely practiced in the art (see, e.g., Henkart, et al., “Cytotoxic T-Lymphocytes” in Fundamental Immunology, Paul (ed.) (2003 Lippincott Williams & Wilkins, Philadelphia, Pa.), pages 1127-50, and references cited therein).
  • Antigen-specific T cell responses are typically determined by comparisons of observed T cell responses according to any of the herein described T cell functional parameters (e.g., proliferation, cytokine release, CTL activity, altered cell surface marker phenotype, etc.) that may be made between T cells that are exposed to a cognate antigen in an appropriate context (e.g., the antigen used to prime or activate the T cells, when presented by immunocompatible antigen-presenting cells) and T cells from the same source population that are exposed instead to a structurally distinct or irrelevant control antigen.
  • a cognate antigen e.g., the antigen used to prime or activate the T cells, when presented by immunocompatible antigen-presenting cells
  • a response to the cognate antigen that is greater, with statistical significance, than the response to the control antigen signifies antigen-specificity.
  • a biological sample may be obtained from a subject for determining the presence and level of an immune response to a Msln peptide as described herein.
  • a “biological sample” as used herein may be a blood sample (from which serum or plasma may be prepared), biopsy specimen, body fluids (e.g., lung lavage, ascites, mucosal washings, synovial fluid, etc.), bone marrow, lymph nodes, tissue explant, organ culture, or any other tissue or cell preparation from the subject or a biological source.
  • Biological samples may also be obtained from the subject prior to receiving any immunogenic composition, which biological sample is useful as a control for establishing baseline (i.e., pre-immunization) data.
  • the subject receiving the subject composition has previously received chemotherapy, such as a lymphodepleting chemotherapy.
  • the lymphodepleting chemotherapy comprises cyclophosphamide, fludarabine, anti-thymocyte globulin, oxaliplatin, or a combination thereof.
  • the subject composition has previously received radiation therapy, immunotherapy comprising a cytokine, an antibody, an antibody-drug conjugate, or Fc fusion protein, antisense nucleotide therapy, gene therapy, a vaccine, or surgery, or any combination thereof.
  • Methods and uses according to this disclosure may further include administering one or more additional agents to treat the disease or disorder in a combination therapy.
  • a combination therapy comprises administering a composition (e.g., any one or more binding protein, modified host cell encoding and/or expressing the same, polynucleotide, vector) with (concurrently, simultaneously, or sequentially) an immune checkpoint inhibitor.
  • a combination therapy comprises administering a composition of the present disclosure with an agonist of a stimulatory immune checkpoint agent.
  • a combination therapy comprises administering a composition of the present disclosure with a secondary therapy, such as chemotherapeutic agent, a radiation therapy, a surgery, an antibody, antibody drug conjugate, a cytokine, an antisense therapy, a gene therapy, a vaccine, or any combination thereof.
  • a secondary therapy such as chemotherapeutic agent, a radiation therapy, a surgery, an antibody, antibody drug conjugate, a cytokine, an antisense therapy, a gene therapy, a vaccine, or any combination thereof.
  • immune suppression agent refers to one or more cells, proteins, molecules, compounds or complexes providing inhibitory signals to assist in controlling or suppressing an immune response.
  • immune suppression agents include those molecules that partially or totally block immune stimulation; decrease, prevent or delay immune activation; or increase, activate, or up regulate immune suppression.
  • immunosuppression agents to target include PD-1, PD-L1, PD-L2, LAG3, CTLA4, B7-H3, B7-H4, CD244/2B4, HVEM, BTLA, CD160, TIM3, GALS, KIR, PVR1G (CD112R), PVRL2, adenosine, A2aR, immunosuppressive cytokines (e.g., IL-10, IL-4, IL-1RA, IL-35), IDO, arginase, VISTA, TIGIT, LAIR1, CEACAM-1, CEACAM-3, CEACAM-5, Treg cells, or any combination thereof.
  • cytokines e.g., IL-10, IL-4, IL-1RA, IL-35
  • IDO arginase
  • VISTA TIGIT
  • LAIR1 CEACAM-1
  • CEACAM-3 CEACAM-5
  • Treg cells or any combination thereof.
  • An immune suppression agent inhibitor may be a compound, an antibody, an antibody fragment or fusion polypeptide (e.g., Fc fusion, such as CTLA4-Fc or LAG3-Fc), an antisense molecule, a ribozyme or RNAi molecule, or a low molecular weight organic molecule.
  • a method may comprise a composition of the present disclosure with one or more inhibitor of any one of the following immune suppression components, singly or in any combination.
  • treatment methods according to the present disclosure may further include administering a PD-1 inhibitor to the subject.
  • the PD-1 inhibitor may include nivolumab (OPDIVO®); pembrolizumab (KEYTRUDA®); ipilimumab+nivolumab (YERVOY®+OPDIVO®); cemiplimab; IBI-308; nivolumab+relatlimab; BCD-100; camrelizumab; JS-001; spartalizumab; tislelizumab; AGEN-2034; BGBA-333+tislelizumab; CBT-501; dostarlimab; durvalumab+MEDI-0680; JNJ-3283; pazopanib hydrochloride+pembrolizumab; pidilizumab; REGN-1979+cemiplimab; ABBV-181; ADUS-100+spart
  • a composition of the present disclosure is used in combination with a LAG3 inhibitor, such as LAG525, IMP321, IMP701, 9H12, BMS-986016, or any combination thereof.
  • a LAG3 inhibitor such as LAG525, IMP321, IMP701, 9H12, BMS-986016, or any combination thereof.
  • a composition of the present disclosure is used in combination with an inhibitor of CTLA4.
  • a composition is used in combination with a CTLA4 specific antibody or binding fragment thereof, such as ipilimumab, tremelimumab, CTLA4-Ig fusion proteins (e.g., abatacept, belatacept), or any combination thereof.
  • a composition of the present disclosure is used in combination with a B7-H3 specific antibody or binding fragment thereof, such as enoblituzumab (MGA271), 376.96, or both.
  • a B7-H4 antibody binding fragment may be a scFv or fusion protein thereof, as described in, for example, Dangaj et al., Cancer Res. 73:4820, 2013, as well as those described in U.S. Pat. No. 9,574,000 and PCT Patent Publication Nos. WO/201740724A1 and WO 2013/025779A1.
  • composition of the present disclosure is used in combination with an inhibitor of CD244.
  • composition of the present disclosure is used in combination with an inhibitor of BLTA, HVEM, CD160, or any combination thereof.
  • Anti CD-160 antibodies are described in, for example, PCT Publication No. WO 2010/084158.
  • composition of the present disclosure is used in combination with an inhibitor of TIM3.
  • composition of the present disclosure is used in combination with an inhibitor of Gal9.
  • composition of the present disclosure is used in combination with an inhibitor of adenosine signaling, such as a decoy adenosine receptor.
  • composition of the present disclosure is used in combination with an inhibitor of A2aR.
  • composition of the present disclosure is used in combination with an inhibitor of KIR, such as lirilumab (BMS-986015).
  • composition of the present disclosure is used in combination with an inhibitor of an inhibitory cytokine (typically, a cytokine other than TGF ⁇ ) or Treg development or activity.
  • an inhibitor of an inhibitory cytokine typically, a cytokine other than TGF ⁇
  • Treg development or activity typically, a cytokine other than TGF ⁇
  • a composition of the present disclosure is used in combination with an IDO inhibitor, such as levo-1-methyl tryptophan, epacadostat (INCB024360; Liu et al., Blood 115:3520-30, 2010), ebselen (Terentis et al., Biochem. 49:591-600, 2010), indoximod, NLG919 (Mautino et al., American Association for Cancer Research 104th Annual Meeting 2013; Apr. 6-10, 2013), 1-methyl-tryptophan (1-MT)-tira-pazamine, or any combination thereof.
  • an IDO inhibitor such as levo-1-methyl tryptophan, epacadostat (INCB024360; Liu et al., Blood 115:3520-30, 2010), ebselen (Terentis et al., Biochem. 49:591-600, 2010), indoximod, NLG919 (Mautino et al., American
  • a composition of the present disclosure is used in combination with an arginase inhibitor, such as N(omega)-Nitro-L-arginine methyl ester (L-NAME), N-omega-hydroxy-nor-1-arginine (nor-NOHA), L-NOHA, 2(S)-amino-6-boronohexanoic acid (ABH), S-(2-boronoethyl)-L-cysteine (BEC), or any combination thereof.
  • an arginase inhibitor such as N(omega)-Nitro-L-arginine methyl ester (L-NAME), N-omega-hydroxy-nor-1-arginine (nor-NOHA), L-NOHA, 2(S)-amino-6-boronohexanoic acid (ABH), S-(2-boronoethyl)-L-cysteine (BEC), or any combination thereof.
  • composition of the present disclosure is used in combination with an inhibitor of VISTA, such as CA-170 (Curis, Lexington, Mass.).
  • composition of the present disclosure is used in combination with an inhibitor of TIGIT such as, for example, COM902 (Compugen, Toronto, Ontario Canada), an inhibitor of CD155, such as, for example, COM701 (Compugen), or both.
  • an inhibitor of TIGIT such as, for example, COM902 (Compugen, Toronto, Ontario Canada)
  • an inhibitor of CD155 such as, for example, COM701 (Compugen)
  • COM701 Compugen
  • composition of the present disclosure is used in combination with an inhibitor of PVRIG, PVRL2, or both.
  • Anti-PVRIG antibodies are described in, for example, PCT Publication No. WO 2016/134333.
  • Anti-PVRL2 antibodies are described in, for example, PCT Publication No. WO 2017/021526.
  • composition of the present disclosure is used in combination with a LAIR1 inhibitor.
  • composition of the present disclosure n is used in combination with an inhibitor of CEACAM-1, CEACAM-3, CEACAM-5, or any combination thereof.
  • a composition of the present disclosure is used in combination with an agent that increases the activity (i.e., is an agonist) of a stimulatory immune checkpoint molecule.
  • a composition can be used in combination with a CD137 (4-1BB) agonist (such as, for example, urelumab), a CD134 (OX-40) agonist (such as, for example, MEDI6469, MEDI6383, or MEDI0562), lenalidomide, pomalidomide, a CD27 agonist (such as, for example, CDX-1127), a CD28 agonist (such as, for example, TGN1412, CD80, or CD86), a CD40 agonist (such as, for example, CP-870,893, rhuCD40L, or SGN-40), a CD122 agonist (such as, for example, IL-2) an agonist of GITR (such as, for example, humanized monoclonal antibodies described in PCT Patent Publication No.
  • a method may comprise administering a composition of the present disclosure with one or more agonist of a stimulatory immune checkpoint molecule, including any of the foregoing, singly or in any combination.
  • a combination therapy comprises a composition of the present disclosure and a secondary therapy comprising one or more of: an antibody or antigen binding-fragment thereof that is specific for a cancer antigen expressed by the non-inflamed solid tumor, a radiation treatment, a surgery, a chemotherapeutic agent, a cytokine, RNAi, or any combination thereof.
  • a combination therapy method comprises administering a composition of the present disclosure and further administering a radiation treatment or a surgery.
  • Radiation therapy is well-known in the art and includes X-ray therapies, such as gamma-irradiation, and radiopharmaceutical therapies.
  • Surgeries and surgical techniques appropriate to treating a given cancer in a subject are well-known to those of ordinary skill in the art.
  • Cytokines useful for promoting immune anticancer or antitumor response include, for example, IFN- ⁇ , IL-2, IL-3, IL-4, IL-10, IL-12, IL-13, IL-15, IL-16, IL-17, IL-18, IL-21, IL-24, and GM-CSF, singly or in any combination with a composition of the present disclosure.
  • a cytokine is administered sequentially, provided that the subject was administered the Msln-specific composition at least three or four times before cytokine administration.
  • the cytokine is administered subcutaneously.
  • the subject may have received or is further receiving an immunosuppressive therapy, such as calcineurin inhibitors, corticosteroids, microtubule inhibitors, low dose of a mycophenolic acid prodrug, or any combination thereof.
  • an immunosuppressive therapy such as calcineurin inhibitors, corticosteroids, microtubule inhibitors, low dose of a mycophenolic acid prodrug, or any combination thereof.
  • the subject being treated has received a non-myeloablative or a myeloablative hematopoietic cell transplant, wherein the treatment may be administered at least two to at least three months after the non-myeloablative hematopoietic cell transplant.
  • a combination therapy method comprises administering a composition of the present disclosure according to the present disclosure and further administering a chemotherapeutic agent.
  • a chemotherapeutic agent includes, but is not limited to, an inhibitor of chromatin function, a topoisomerase inhibitor, a microtubule inhibiting drug, a DNA damaging agent, an antimetabolite (such as folate antagonists, pyrimidine analogs, purine analogs, and sugar-modified analogs), a DNA synthesis inhibitor, a DNA interactive agent (such as an intercalating agent), and a DNA repair inhibitor.
  • Illustrative chemotherapeutic agents include, without limitation, the following groups: anti-metabolites/anti-cancer agents, such as pyrimidine analogs (5-fluorouracil, floxuridine, capecitabine, gemcitabine and cytarabine) and purine analogs, folate antagonists and related inhibitors (mercaptopurine, thioguanine, pentostatin and 2-chlorodeoxyadenosine (cladribine)); antiproliferative/antimitotic agents including natural products such as vinca alkaloids (vinblastine, vincristine, and vinorelbine), microtubule disruptors such as taxane (paclitaxel, docetaxel), vincristin, vinblastin, nocodazole, epothilones and navelbine, epidipodophyllotoxins (etoposide, teniposide), DNA damaging agents (actinomycin, amsacrine, anthracyclines, bleomycin, bus
  • therapy further comprises administering a T cell based vaccine may be used (see, e.g., PCT Publication No. WO 2017/192924, of which the T cell vaccines, immunogenicity enhancers, transposon expression constructs, and related methods are incorporated by reference in their entireties entirety).
  • a vaccine compoistion comprises a liposomal RNA preparation (see, e.g., Kreiter, et al, Nature 520: 692, 2015, which preparations and methods of making the same are incorporated by reference herein in their entireties).
  • an vaccine composition is used to prepare a peptide-pulsed dendritic cell or other antigen-presenting cell, which may be performed ex vivo, in vitro, or in vivo.
  • the present disclosure also provides a method for preparing antigen-pulsed antigen-presenting cells.
  • the methods comprise contacting in vitro, under conditions and for a time sufficient for antigen processing and presentation by antigen-presenting cells to take place, (i) a population of antigen-presenting cells that are immunocompatible with a subject, and (ii) a polynucleotide, peptide, immunogenic composition, and/or an expression vector as described herein, thereby obtaining antigen-pulsed antigen-presenting cells capable of eliciting an antigen-specific T-cell response to a Msln peptide as described herein.
  • the method may further include contacting the antigen-pulsed antigen-presenting cells with one or a plurality of immunocompatible T cells under conditions and for a time sufficient to generate Msln-specific T cells.
  • the method further comprises transfecting or transducing a population of immune cells in vitro or ex vivo with a polynucleotide comprising the binding protein-encoding nucleic acid sequence so-determined, thereby obtaining a population of engineered Msln-specific immune cells, optionally in an amount effective to adoptively transfer or confer an antigen-specific T-cell response to a Msln antigen when the cells are administered to a subject.
  • immune cell lines may be generated as described by Ho, et al. (see 2006 J Immunol Methods 310 (1-2):40-52)).
  • DCs dendritic cells
  • PBMCs plastic adherent fraction of PBMCs by culture over two days (days ⁇ 2 to 0) in DC media (CELLGENIXTM, Freiburg, Germany) supplemented with GM-CSF (800 U/ml) and IL-4 (1000 U/ml).
  • GM-CSF 800 U/ml
  • IL-4 1000 U/ml
  • maturation cytokines TNF ⁇ (1100 U/ml), IL-1 ⁇ (2000 U/ml), IL-6 (1000 U/ml) and PGE2 (1 ⁇ g/ml) can be added.
  • CD8 T cells can be isolated from PBMCs using anti-CD8 microbeads (MILTENYI BIOTECTM, Auburn, Calif.) and stimulated with DCs at an effector target (E:T) ratio of 1:5 to 1:10 in the presence of IL-21 (30 ng/ml).
  • E:T effector target
  • IL-2 (12.5 U/ml
  • IL-7 (5 ng/ml)
  • IL-15 5 ng/ml
  • Cells may be restimulated between days 10 and 14 using the plastic adherent faction of irradiated autologous PBMCs as antigen presenting cells (APCs) after being peptide-pulsed for two hours and in the presence of IL-21. After restimulation, cells can be supplemented from day 1 on with IL-2 (25 U/ml), IL-7 (5 ng/ml), and IL-15 (5 ng/ml).
  • IL-2 25 U/ml
  • IL-7 5 ng/ml
  • IL-15 5 ng/ml
  • T-cell clones can be generated by plating cells at limiting dilution and expanding with TM-LCLs coated with OKT3 (ORTHO BIOTECHTM, Bridgewater, N.J.) and allogeneic PBMCs as feeders (REP protocol) as described (see Ho, et al., 2006 J Immunol Methods 310 (1-2):40-52).
  • the present disclosure provides, among other embodiments, the following embodiments.
  • a binding protein comprising a T cell receptor (TCR) ⁇ -chain variable domain (V ⁇ ) and a TCR ⁇ -chain variable domain (V ⁇ ), wherein: (a) the V ⁇ comprises the CDR3 amino acid sequence set forth in SEQ ID NO:39 or 37, and the V ⁇ optionally comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:101 or 99; (b) the V ⁇ comprises the CDR3 amino acid sequence set forth in SEQ ID NO:40 or SEQ ID NO:38, and the V ⁇ optionally comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:102 or 100; and/or (c) the V ⁇ comprises the CDR3 amino acid sequence set forth in SEQ ID NO:39 or 37, and the V ⁇ comprises the CDR3 amino acid sequence set forth in SEQ ID NO:40 or 38, wherein the binding protein is capable of specifically binding to a meso
  • the V ⁇ of (a), (b), and/or (c) of a binding protein as disclosed herein comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:102 or 100, provided that at least three or four of the CDRs have no change in sequence, wherein the CDRs that do have sequence changes have only up to two amino acid substitutions, up to a contiguous five amino acid deletion, or a combination thereof; and/or (ii) the V ⁇ of (a), (b), and/or (c) of a binding protein as disclosed herein comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:101 or 99, provided that at least three or four of the CDRs have no change in sequence, wherein the CDRs that do have sequence changes have only up to two amino acid substitutions, up to a contiguous five amino acid deletion, or a combination thereof.
  • the binding protein referred to with respect to an embodiment may comprise: (a) the CDR1 ⁇ amino acid sequence set forth in SEQ ID NO:93; (b) the CDR2 ⁇ amino acid sequence set forth in SEQ ID NO:94; (c) the CDR3 ⁇ amino acid sequence set forth in SEQ ID NO:39; (d) a CDR1 ⁇ amino acid sequence set forth in SEQ ID NO:83, optionally as set forth in SEQ ID NO:84, further optionally as set forth in SEQ ID NO:91; (e) the CDR2 ⁇ amino acid sequence set forth in SEQ ID NO:92; and (f) the CDR3 ⁇ amino acid sequence set forth in SEQ ID NO:40.
  • the binding protein referred to with respect to an embodiment may comprise an amino acid sequence having at least 85% identity to an amino acid sequence encoded by: (a) TRBJ2-3*01; (b) TRAV21*01 or TRAV21*02; (c) TRBV5-4*01; (d) TRAJ57*01; and/or (e) TRBD1*01 or TRBD2*02. Still further, the binding protein referred to with respect to an embodiment may comprise a V ⁇ comprising an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:102, and a V ⁇ comprising an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:101.
  • an embodiment may comprise a binding protein wherein the V ⁇ comprises or consists of the amino acid sequence set forth in SEQ ID NO:102, and wherein the V ⁇ comprises or consists of the amino acid sequence set forth in SEQ ID NO:101.
  • the binding protein in an embodiment may comprise a TCR ⁇ chain (TCR ⁇ ) and a TCR chain (TCR ⁇ ), wherein the TCR ⁇ comprises or consists of an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:110 or 29, and/or wherein the TCR ⁇ comprises or consists of an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:109 or 28.
  • Some embodiments may comprise a binding protein wherein the TCR ⁇ comprises or consists of the amino acid sequence set forth in SEQ ID NO:110 or 29, and wherein the TCR ⁇ comprises or consists of the amino acid sequence set forth in SEQ ID NO:109 or 28.
  • the binding protein comprises: (a) a CDR1 ⁇ amino acid sequence as set forth in SEQ ID NO:89; (b) a CDR2 ⁇ amino acid sequence as set forth in SEQ ID NO:90; (c) a CDR3 ⁇ amino acid sequence as set forth in SEQ ID NO:37; (d) a CDR1 ⁇ amino acid sequence as set forth in SEQ ID NO:83, optionally as set forth in SEQ ID NO:87; (e) a CDR2 ⁇ amino acid sequence as set forth in SEQ ID NO:88; and (f) a CDR3 ⁇ amino acid sequence as set forth in SEQ ID NO:38.
  • the binding protein may comprise an amino acid sequence having at least 85% identity to an amino acid sequence encoded by: (a) TRBJ1-1*01 or TRBJ2-3*01; (b) TRAV4-1*01; (c) TRAJ18*01; and/or (d) TRBD1*01 or TRBD2*02.
  • the binding protein may comprise a V ⁇ that comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:100 and the V ⁇ comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:99.
  • the binding protein may comprise a V ⁇ that comprises or consists of the amino acid sequence set forth in SEQ ID NO:100, and wherein the V ⁇ comprises or consists of the amino acid sequence set forth in SEQ ID NO:99.
  • the binding protein comprises a TCR ⁇ chain (TCR ⁇ ) and a TCR ⁇ chain (TCR ⁇ ), wherein the TCR ⁇ comprises or consists of an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:108 or 23, and/or wherein the TCR ⁇ comprises or consists of an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:107 or 22.
  • the binding protein comprises a TCR ⁇ that comprises or consists of the amino acid sequence set forth in SEQ ID NO:108 or 23, and wherein the TCR ⁇ comprises or consists of the amino acid sequence set forth in SEQ ID NO:107 or 22.
  • the binding protein comprises a binding protein that is capable specifically binding to a SEQ ID NO:32:human leukocyte antigen (HLA) complex, and in some such instances the HLA comprises HLA-A*201.
  • HLA human leukocyte antigen
  • alanine mutagenesis of any one or more of residues 3, 5, 6, or 9 of SEQ ID NO:32 does not abrogate or does not substantially impair binding by the binding protein to the Msln peptide:HLA complex.
  • the binding protein is capable of binding to a peptide:HLA complex wherein the peptide comprises or consists of the consensus amino acid sequence set forth in SEQ ID NO:61.
  • alanine mutagenesis of any one or more of residues 1, 5, or 9 of SEQ ID NO:32 does not abrogate or does not substantially impair binding by the binding protein to the Msln peptide:HLA complex.
  • the binding protein is capable of binding to a peptide:HLA complex wherein the peptide comprises or consists of the consensus amino acid sequence set forth in SEQ ID NO:62.
  • the binding protein does not bind to, or does not specifically bind to, a peptide:HLA complex, wherein the peptide comprises or consists of the amino acid sequence set forth in any one or more of SEQ ID NOs:63-77, and wherein the HLA is optionally HLA-A:02*01.
  • a binding protein comprises a T cell receptor (TCR) ⁇ -chain variable domain (V ⁇ ) and a TCR ⁇ -chain variable domain (V ⁇ ), wherein: (a) the V ⁇ comprises the CDR3 amino acid sequence set forth in SEQ ID NO:33 or 35, and the V ⁇ optionally comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:95 or 97; (b) the V ⁇ comprises the CDR3 amino acid sequence set forth in SEQ ID NO: 34 or 36, and the V ⁇ optionally comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:96 or 98; and/or (c) the V ⁇ comprises the CDR3 amino acid sequence shown in SEQ ID NO:33 or 35, and the V ⁇ comprises the CDR3 amino acid sequence shown in SEQ ID NO:40 or 38, wherein the binding protein is capable of specifically binding to a mesothelin (Msln
  • the V ⁇ of (a), (b), and/or (c) comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:96 or 98, provided that at least three or four of the CDRs have no change in sequence, wherein the CDRs that do have sequence changes have only up to two amino acid substitutions, up to a contiguous five amino acid deletion, or a combination thereof; and/or (ii) the V ⁇ of (a), (b), and/or (c) comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:95 or 97, provided that at least three or four of the CDRs have no change in sequence, wherein the CDRs that do have sequence changes have only up to two amino acid substitutions, up to a contiguous five amino acid deletion, or a combination thereof.
  • the binding protein comprises: (a) the CDR1 ⁇ amino acid sequence set forth in SEQ ID NO:80; (b) the CDR2 ⁇ amino acid sequence set forth in SEQ ID NO:81 or 118; (c) the CDR3 ⁇ amino acid sequence set forth in SEQ ID NO:33; (d) a CDR1 ⁇ amino acid sequence as set forth in SEQ ID NO:83, optionally as set forth in SEQ ID NO:84, further optionally as set forth in SEQ ID NO:78; (e) the CDR2 ⁇ amino acid sequence set forth in SEQ ID NO:79; and (f) the CDR3 ⁇ amino acid sequence set forth in SEQ ID NO:34.
  • the binding protein comprises an amino acid sequence having at least 85% identity to an amino acid sequence encoded by: (a) TRBJ2-7*01 or TRBJ2-3*01; (b) TRAV1-1*01; (c) TRBV12-4*01; (d) TRAJ3*01; and/or (e) TRBD1*01 or TRBD2*02.
  • the binding protein comprises a V ⁇ that comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:96, and a V ⁇ that comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:95.
  • the binding protein comprises a V ⁇ that comprises or consists of the amino acid sequence set forth in SEQ ID NO:96, and a V ⁇ that comprises or consists of the amino acid sequence set forth in SEQ ID NO:95.
  • the binding protein comprises a TCR ⁇ chain (TCR ⁇ ) and a TCR ⁇ chain (TCR ⁇ ), wherein the TCR ⁇ comprises or consists of an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:104 or 7, and/or wherein the TCR ⁇ comprises or consists of an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:103 or 6.
  • the binding protein comprises a TCR ⁇ that comprises or consists of the amino acid sequence set forth in SEQ ID NO:104 or 7, and wherein the TCR ⁇ comprises or consists of the amino acid sequence set forth in SEQ ID NO:103 or 106.
  • the binding protein comprises: (a) the CDR1 ⁇ amino acid sequence set forth in SEQ ID NO:85; (b) the CDR2 ⁇ amino acid sequence set forth in SEQ ID NO:86 or 119; (c) the CDR3 ⁇ amino acid sequence set forth in SEQ ID NO:35; (d) a CDR1 ⁇ amino acid sequence set forth in SEQ ID NO:83, optionally as set forth in SEQ ID NO:84, further optionally as set forth in SEQ ID NO:82; (e) the CDR2 ⁇ amino acid sequence set forth in SEQ ID NO:79; and (f) the CDR3 ⁇ amino acid sequence set forth in SEQ ID NO:36.
  • the binding protein comprises an amino acid sequence having at least 85% identity to an amino acid sequence encoded by: (a) TRBJ2-3*01; (b) TRAV12-3*01; (c) TRBV12-3*01; (d) TRAJ29*01; and/or (e) TRBD1*01 or TRBD2*02.
  • the binding protein comprises a V ⁇ that comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:98 and a V ⁇ that comprises an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:97.
  • the binding protein comprises a V ⁇ that comprises or consists the amino acid sequence set forth in SEQ ID NO:98, and a V ⁇ that comprises or consists the amino acid sequence set forth in SEQ ID NO:97.
  • the binding protein comprises a TCR ⁇ chain (TCR ⁇ ) and a TCR ⁇ chain (TCR ⁇ ), wherein the TCR ⁇ comprises or consists of an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:106 or 15, and/or wherein the TCR ⁇ comprises or consists of an amino acid sequence having at least about 85% identity to the amino acid sequence set forth in SEQ ID NO:105 or 14.
  • the binding protein comprises a TCR ⁇ that comprises or consists the amino acid sequence set forth in SEQ ID NO:106 or 15, and a TCR ⁇ that comprises or consists of the amino acid sequence set forth in SEQ ID NO:105 or 14.
  • the binding protein is capable specifically binding to a SEQ ID NO:31:human leukocyte antigen (HLA) complex, and wherein the HLA is optionally HLA-A*201.
  • the binding protein is or comprises a TCR, wherein the TCR is optionally soluble, an antigen-binding fragment of a TCR, a scTCR, or CAR.
  • the binding protein is human, humanized, or chimeric.
  • the binding protein is capable of binding to the mesothelin:HLA complex in the absence of, or independent of, CD8.
  • the binding protein has a Msln peptide EC50 of about 9 ⁇ M, about 8 ⁇ M, about 7 ⁇ M, about 6 ⁇ M, about 5 ⁇ M, about 4 ⁇ M, about 3 ⁇ M, about 2 ⁇ M, about 1 ⁇ M, about 0.9 ⁇ M, about 0.8 ⁇ M, about 0.7 ⁇ M, about 0.6 ⁇ M, about 0.5 ⁇ M, about 0.4 ⁇ M, about 0.3 ⁇ M, about 0.2 ⁇ M, or less.
  • composition that comprises a binding protein described herein and a pharmaceutically acceptable carrier, diluent, or excipient.
  • a polynucleotide encodes a binding protein described herein.
  • the polynucleotide is codon optimized for expression in a host cell, wherein the host cell is optionally a human immune system cell, preferably a T cell.
  • the polynucleotide has at least about 50% identity to the polynucleotide sequence set forth in any one of SEQ ID NOs:1-4, 9-12, 17-20, 25, and 26.
  • the polynucleotide comprises a TCR ⁇ chain-encoding polynucleotide and a TCR ⁇ chain-encoding polynucleotide that have at least about 50% identity to the polynucleotide sequences set forth in SEQ ID NOs: (i) 1 and 3, respectively; (ii) 2 and 4, respectively; (iii) 9 and 11, respectively; (iv) 10 and 12, respectively; (v) 17 and 19, respectively; (vi) 18 and 20, respectively; or (vii) 25 and 26, respectively.
  • the polynucleotide comprises a polynucleotide that encodes a self-cleaving peptide disposed between a TCR ⁇ chain-encoding polynucleotide and a TCR ⁇ chain-encoding polynucleotide.
  • the encoded polypeptide comprises the amino acid sequence as set forth in any one of SEQ ID NOs:8, 16, 24, and 30.
  • the polynucleotide encoding the binding protein has at least about 50% identity to the polynucleotide sequence as set forth in any one of SEQ ID NOs:5, 13, 21, 27, and 120.
  • a polynucleotide encoding a binding protein comprises or consists of the polynucleotide sequence set forth in SEQ ID NO:120.
  • an expression vector that comprises a polynucleotide described herein operably linked to an expression control sequence.
  • the expression vector is capable of delivering the polynucleotide to a host cell.
  • the host cell is a hematopoietic progenitor cell or a human immune system cell.
  • the immune system cell is a CD4+ T cell, a CD8+ T cell, a CD4 ⁇ CD8 ⁇ double negative T cell, a ⁇ T cell, a natural killer cell, a natural killer T cell, a macrophage, a dendritic cell, or any combination thereof.
  • the immune system cell is a na ⁇ ve T cell, a central memory T cell, a stem cell memory T cell, an effector memory T cell, or any combination thereof.
  • the expression vector is a viral vector.
  • the viral vector is a lentiviral vector or a ⁇ -retroviral vector.
  • a recombinant host cell comprises a heterologous polynucleotide encoding a binding protein as described herein and/or an expression vector as described herein, wherein the recombinant host cell is capable of expressing on its cell surface the encoded binding protein.
  • the recombinant host cell is a hematopoietic progenitor cell or a human immune system cell.
  • the recombinant host cell is a CD4+ T cell, a CD8+ T cell, a CD4 ⁇ CD8 ⁇ double negative T cell, a ⁇ T cell, a natural killer cell, a natural killer T cell, a macrophage, a dendritic cell, or any combination thereof.
  • the recombinant host cell is a T cell. In some embodiments, the recombinant host cell is a na ⁇ ve T cell, a central memory T cell, a stem cell memory T cell, an effector memory T cell, or any combination thereof. In some embodiments, the recombinant host cell is a T cell or a NK-T cell encoding an endogenous TCR, and wherein the mesothelin-specific binding protein encoded by the heterologous polynucleotide is capable of more efficiently associating with a CD3 protein as compared to the endogenous TCR.
  • Nur77 expression is increased in the recombinant host cell when the host cell is in the presence of the Msln peptide bound by the encoded binding protein at a concentration of about 10 ⁇ 2 ⁇ M peptide, about 10 ⁇ 1 ⁇ M peptide, about 1 ⁇ M peptide, or about 10 1 ⁇ M peptide, wherein the peptide is optionally presented to the host cell by an antigen presenting cell.
  • the recombinant host cell is one wherein the recombinant host cell does not produce IFN- ⁇ and/or does not exhibit activation and/or cytotoxic activity when contacted with a cell expressing: (i) HLA-C6:02:01; (ii) HLA-B13:01:01 without HLA-B13:02:01; (iii) HLA-A3; (iv)
  • the recombinant host cell comprises T cell or a NK-T cell encoding an endogenous TCR, wherein the binding protein encoded by the heterologous polynucleotide has higher cell surface expression as compared to the endogenous TCR.
  • a cell composition comprising a recombinant host cell described herein and a pharmaceutically acceptable carrier, excipient, or diluent.
  • a unit dose comprises an effective amount of a recombinant host cell or a cell composition described herein.
  • a method of treating a disease or disorder associated with mesothelin expression and/or activity in a subject comprises: administering to the subject an effective amount of the binding protein described herein, the recombinant host cell described herein, the composition described herein, or the unit dose of described herein.
  • the method comprises a method of treating a disease or disorder associated with mesothelin expression and/or activity in a subject, wherein the disease or disorder is a hyperproliferative disease or a proliferative disease.
  • the method comprises a method of treating a disease or disorder associated with mesothelin expression and/or activity in a subject, wherein the disease or disorder is a cancer and, optionally, the cancer is a solid cancer or a hematological malignancy.
  • the method comprises a method of treating a disease or disorder associated with mesothelin expression and/or activity in a subject, wherein the disease or disorder is one of biliary cancer, bladder cancer, bone and soft tissue carcinoma, brain tumor, breast cancer, cervical cancer, colon cancer, colorectal adenocarcinoma, colorectal cancer, desmoid tumor, embryonal cancer, endometrial cancer, esophageal cancer, gastric cancer, gastric adenocarcinoma, glioblastoma multiforme, gynecological tumor, head and neck squamous cell carcinoma, hepatic cancer, lung cancer, mesothelioma, malignant melanoma, osteosarcoma, ovarian cancer, pancreatic cancer, pancreatic ductal adenocarcinoma, primary astrocytic tumor, primary thyroid cancer, prostate cancer, renal cancer, renal cell carcinoma, rhabdomyosarcoma, skin cancer, soft tissue
  • the method comprises a method of treating a disease or disorder associated with mesothelin expression and/or activity in a subject, wherein the disease or disorder is one of pancreatic cancer, ovarian cancer, breast cancer, gastric cancer, colorectal cancer, mesothelioma, or lung cancer.
  • the binding protein, host cell, composition, or unit dose is administered parenterally or intravenously.
  • the method comprises administering a plurality of doses of the binding protein, host cell, composition, or unit dose to the subject and, optionally, the plurality of doses are administered at intervals between administrations of about two to about four weeks.
  • method further comprises administering a cytokine to the subject.
  • the method comprises administering IL-2, IL-15, IL-21, or any combination thereof.
  • the method comprises a subject that is further receiving or has received an immune checkpoint inhibitor, an agonist of a stimulatory immune checkpoint agent, radiation therapy, an antibody, an antibody-drug conjugate, an Fc fusion protein, an antisense nucleotide therapy, a gene therapy, a vaccine, a surgery, a chemotherapy, or any combination thereof.
  • the binding protein described herein, the composition described herein, the polynucleotide described herein, the expression vector described herein, the recombinant host cell described herein, the cell composition described herein, or the unit dose described herein is for use in the treatment of a disease or disorder characterized by mesothelin expression and/or activity.
  • the binding protein described herein, the composition described herein, the polynucleotide described herein, the expression vector described herein, the recombinant host cell described herein, the cell composition described herein, or the unit dose described herein is for use in adoptive immunotherapy of a disease or disorder characterized by mesothelin expression and/or activity.
  • the binding protein described herein, the composition described herein, the polynucleotide described herein, the expression vector described herein, the recombinant host cell described herein, the cell composition described herein, or the unit dose described herein is for use in the manufacture of a medicament for treating a disease or disorder characterized by mesothelin expression and/or activity.
  • the binding protein, composition, polynucleotide, expression vector, recombinant host cell, cell composition, or unit dose for use described herein wherein the disease or disorder characterized by mesothelin expression and/or activity is mesothelioma, pancreatic cancer, ovarian cancer, lung cancer, a cancer wherein an Msln 20-28 peptide is expressed on a tumor cell of the cancer, or a cancer wherein an Msln 530-538 peptide is expressed on a tumor cell of the cancer.
  • an isolated polynucleotide that encodes a binding protein that is capable of specifically binding to a SEQ ID NO:32:HLA-A:02*01 complex, wherein the polynucleotide comprises or consists of the polynucleotide sequence set forth in SEQ ID NO:120.
  • an expression vector comprising the polynucleotide that encodes a binding protein that is capable of specifically binding to a SEQ ID NO:32:HLA-A:02*01 complex is provided, wherein the polynucleotide comprises or consists of the polynucleotide sequence set forth in SEQ ID NO:120 operably linked to an expression control sequence.
  • the expression vector is capable of delivering the polynucleotide to a host cell.
  • the host cell is a hematopoietic progenitor cell or a human immune system cell.
  • the expression vector immune system cell is a CD4+ T cell, a CD8+ T cell, a CD4 ⁇ CD8 ⁇ double negative T cell, a ⁇ T cell, a natural killer cell, a natural killer T cell, a macrophage, a dendritic cell, or any combination thereof.
  • the expression vector immune system cell is a na ⁇ ve T cell, a central memory T cell, a stem cell memory T cell, an effector memory T cell, or any combination thereof.
  • the expression vector of any one of claims 86 - 90 wherein the expression vector is a viral vector.
  • the expression vector is a viral vector that is a lentiviral vector or a ⁇ -retroviral vector.
  • a recombinant host cell comprising the polynucleotide described herein and/or the expression vector described herein, wherein the recombinant host cell is capable of expressing on its cell surface the encoded binding protein.
  • the recombinant host cell is a hematopoietic progenitor cell or a human immune system cell.
  • recombinant host cell is an immune system cell is a CD4+ T cell, a CD8+ T cell, a CD4 ⁇ CD8 ⁇ double negative T cell, a ⁇ T cell, a natural killer cell, a natural killer T cell, a macrophage, a dendritic cell, or any combination thereof.
  • the recombinant host cell is a T cell.
  • the recombinant host cell is a na ⁇ ve T cell, a central memory T cell, a stem cell memory T cell, an effector memory T cell, or any combination thereof.
  • Exemplary TCR clones specific for Msln 20 or Msln 530 are shown in FIGS. 1A and 1B , respectively, and the enrichment score of each TCR clonotype in the next-generation sequencing (NGS) based method for TCR isolation presented herein is compared to T cell frequency.
  • the enrichment score on the y-axis correlates with the magnitude of binding to peptide:HLA tetramer.
  • All TCRs were synthesized and tested for function when expressed in reporter T cell lines and primary CD8 + PBMCs. The TCRs with the highest functional avidity when transferred into recipient CD8 + T cells are encircled.
  • Msln 530 -specific TCR coding constructs were lentivirally transduced into CD8 ⁇ Jurkat T cells that lack endogenous TCR ⁇ / ⁇ chains (Jurkat76—dark gray plots) or Jurkat76 cells transduced to express CD8 ⁇ (Jurkat76-CD8 ⁇ —light gray plots) (see FIG. 2 ).
  • CD3 cannot be expressed at the cell surface. Therefore, CD3 expression is a proxy for TCR surface expression in these cells, allowing tetramer binding to be assessed relative to TCR surface expression.
  • TCRs are presented in order of tetramer binding relative to CD3 expression, and TCRs above the indicated line are considered to be CD8-independent, characteristic of high affinity.
  • TCRs that exhibited the highest level of tetramer binding were evaluated for antigen-specific function using a reporter Jurkat T cell line that has a tdTomato transgene knocked into the Nur77 locus.
  • T2 target cells were pulsed with titrated concentrations of peptide and TCR-expressing T cells were assessed for tdTomato expression, as indicated in FIG. 3A .
  • the percentage of tdTomato-positive cells detected at each peptide concentration was plotted and fit to a dose-response curve by non-linear regression ( FIG. 3B ).
  • TCR B11 also referred to herein as 11B
  • TCR B11 also referred to herein as 11B
  • the two TCRs with the highest level of tetramer binding were found to have lower antigen sensitivity, and are also indicated by arrows in FIG. 3B .
  • CD8 + T cells were purified from donor PBMCs and lentivirally transduced with TCRs specific for Msln 530 or Msln 20 (which were selected through a similar process to that described in Examples 3 and 4). After 8 days, tetramer hi cells were sorted and further expanded for 8-10 days. Transduced T cells were stained with tetramer and CD8 to confirm purity and uniform high level CD8 expression.
  • the percentage of IFN- ⁇ -positive cells detected at each peptide concentration was plotted and fit to a dose-response curve by non-linear regression.
  • the calculated EC50 for each TCR was plotted.
  • the most avid TCR specific for each epitope (“20-B3” and “530-B11”, respectively) is indicated with an arrow.
  • FIG. 8 demonstrates an epitope analysis assay in which each successive amino acid of the Mlsn target peptide sequence was replaced by an alanine and TCR-transduced T cells were incubated with HLA-A2 + target cells pulsed with the variant peptide. Representative data of IFN- ⁇ production in response to each variant peptide by a Msln 20 -specific TCR is shown at the bottom of the figure.
  • results of the alanine scan assay showing the percent IFN- ⁇ + T cells in response to each alanine-substituted peptide for each of the four tested TCRs are shown in FIGS. 9A-9D .
  • the essential residues are identified by their one-letter amino acid code and the non-essential residues are indicated by an X.
  • Human peptides predicted to have potential cross-reactivity with Msln-specific TCRs were identified using the ScanProsite tool by searching the human proteome for the indicated consensus epitope motif of each of the indicated Msln 530 -specific TCRs (A11 and B11), as illustrated in FIG. 10 .
  • Resulting peptides were analyzed for HLA-A2 binding using three different prediction algorithms: SITHPATHI, PanMHCnet, and IEDB. The recommended cutoff for each approach is listed in parenthesis next to the name of the algorithm.
  • Potential cross-reacting peptides are as indicated in the figure key, and were synthesized for further analysis.
  • a high dose of peptide (10 ⁇ M) was used in order to detect potential reactivities.
  • the percentage of IFN- ⁇ -positive TCR-transduced T cells is shown in FIG. 11A for Msln 530 -11A and Msln 530 -11B.
  • the response with 10 ⁇ M of the wildtype Msln 530 peptide, and the maximal response obtained with a non-specific T cell activation cocktail are shown on the right side of the graph. Only one peptide (#10) elicited a low level ( ⁇ 20%) response from TCR Msln 530 -11B-transduced T cells at 10 ⁇ M peptide.
  • the graph in FIG. 11B shows a dose-response curve for Msln 530 -11B transduced T cell reactivity to the Msln 530 peptide versus several potential cross-reactive peptides, including peptide #10, to determine reactivity at physiological levels.
  • the percent IFN- ⁇ + data was fit to dose-response curves by non-linear regression, and EC50 values were calculated and are shown below the graph. These data show that the Msln 530 -11B EC50 for peptide #10 is more than 3000 ⁇ higher than for that of Msln 530 ; therefore, Msln 530 -11B has much greater specificity for Msln 530 than for peptide #10.
  • TCR-transduced T cells were cultured with allogeneic LCLs that naturally express diverse HLA alleles, including many of the more common alleles.
  • the LCL lines and corresponding HLA allele expression are listed in the table in FIG. 12A .
  • FIGS. 12B-12I For each cell line ( FIGS. 12B-12I ), the percentage of IFN- ⁇ expression is shown when the T cells and LCL cells were co-cultured in the presence or absence of added Msln 530 peptide (which is presented by the transduced T cells when the LCL cell line lacks HLA-A2 expression).
  • FIGS. 13A-13H Further analysis of T cell targeting of diverse LCL cell lines is shown in FIGS. 13A-13H .
  • TCR-transduced T cells were cultured with allogeneic LCLs that naturally express diverse HLA alleles, including many of the more common alleles.
  • the LCL lines and corresponding HLA allele expression are listed in the table in FIG. 13A .
  • the percentage IFN- ⁇ expression is shown following co-culture of target and effector cells in the presence or absence of added Msln 530 peptide (which is presented by the transduced T cells when the LCL cell lines lack HLA-A2 expression).
  • This second set of LCLs include several lines that express HLA-C6 and HLA-B13, which exhibit linkage disequilibrium and are commonly found together. Several of these LCLs elicited a response from Msln 530 -11B-transduced T cells. These data show that HLA-B13:02:01 is the alloreactive allele, since only cells that express HLA-B13:02:01 elicit a response, while cells expressing HLA-C6:02:01 or HLA-B13:01:01 without HLA-B13:02:01 do not elicit a response.
  • Table 1 shows the frequency of HLA-B13:02:01 and HLA-A2:01:01 co-expression in different populations. Some alloreactivity specific to HLA-B13:02:01 was detected. However, given the small haplotype frequency within the population, it is a rare event for a patient to present with an allele that is cross-reactive.

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BR112021008973A2 (pt) 2021-10-26
SG11202104349QA (en) 2021-05-28
AU2019377553A1 (en) 2021-05-27
CN113286815B (zh) 2024-04-26
WO2020097530A3 (en) 2020-07-23
BR112021008973A8 (pt) 2023-05-02
KR20210102231A (ko) 2021-08-19
CN113286815A (zh) 2021-08-20
EP3877404A2 (en) 2021-09-15
JP7558935B2 (ja) 2024-10-01
EA202191012A1 (ru) 2021-08-17
MX2021005308A (es) 2021-09-08

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